BioSystems, 29 (1993) 105-128 105

Elsevier Scientific Publishers Ireland Ltd.

A linguistic representation of the regulation of transcription

initiation. II. Distinctive features of sigma 70 promoters and
their regulatory binding sites

Julio Collado-Vides
Centro de Investigacidn sobre Fijacidn de Nitrdgeno, Universidad Nacional Autdnoma de Mdxico, Cuernavaca A.P. 565-.4,
Morelos 62271 (Mdxico)

(Received December 5th, 1992)

The goal of this paper and the accompanying one is to achieve a linguistic representation of a set of sigma 70 promoters.
Such a description is formed by an ordered concatenated array of complex symbols identified by their categorical property,
i.e. promoter, operator, activator binding site, etc. Each of these symbols may contain several properties associated with their
respective classes of 'molecular words'. The main problem in attaining such a description is to define which properties are going
to be represented, and how. In the accompanying paper the criteria on which the selection of alternative descriptions is based
were discussed. The properties of promoters and regulatory sites are discussed here, and their corresponding distinctive fea-
tures are selected following such criteria. Thus, information that is not directly relevant and that can overspecify the descrip-
tion has been excluded, since it does not seem to contribute to identifying classes of substitutable elements. Other properties,
such as strength of promoters, position of regulatory sites, different types of specificities of regulatory proteins, affinity of their
binding sites, etc., are also discussed. As a result of this analysis, a complete representation with distinctive features of the
set of sigma 70 promoters is attainable.

Key words: Linguistic formalisation; Gene regulation; Bacterial promoters

1. Introduction in molecular biology. Certainly the catalogue of

This and the accompanying paper (Part I) con-
tain a linguistic analysis that is required for the
further development of a grammar of sigma 70
promoters regulated at the initiation of tran-
scription (Collado-Vides, 1992). We refer to
operons, transcription units, promoters and
structural genes and their closely associated
regulatory sites as units of genetic information
(UGIs).
The question of constructing grammatical
models or grammars illustrates, in a smaller
scale, the problem of integration of information
Correspondence to: Julio Collado-Vides, Centro de Investiga-
ci6n sobre Fijaci6n de Nitr6geno, Universidad Nacional
AutSnoma de M~xico, Cuernavaca A.P. 565-A, Morelos
62271, M~xico.
promoters raised the question of how to
organize such a collection of different arrays
under a common set of principles. The question
is how similar types of data sets can be used to
construct a linguistic formalisation where all the
pertinent properties of gene regulation are
made explicit.
The linguistic approach enables us to address
in a systematic way the question of how the
huge amount of already deciphered information
can be integrated in order to enhance our bio-
logical understanding. These two papers are
devoted to defining a transcript, or representa-
tion of UGIs, into elements that are pertinent to
the functioning of the sigma 70 reading appara-
tus. We call it a linguistic L1 level of represen-
tation of UGIs. The identification of such
representation consists in selecting which infor-
106
mation is pertinent to the regulatory description
of UGIs, and which is the best way to describe it.
The purpose of this paper is to identify the set
of distinctive features, of promoters (Pr),
operators (Op) and activator binding sites (I) of
sigma 70 promoters. This identification is based
on the criteria stipulated in the previous paper.
As mentioned before, the set of distinctive fea-
tures of molecular categories is going to include
properties of the nucleotide sequences of DNA
as well as properties of the respective proteins.
2. Distinctive features of the Pr category
In the previous paper we determined the way
information on co-ordinates of sites is included
as a distinctive feature. In this section we will
discuss the way several properties of promoter
categories are incorporated as distinctive fea-
tures. We will discuss differences in sigma fac-
tor specificity, and will analyse whether notions
such as lac, narG and malE (see (10), (11) and
(13) in the accompanying paper) that identify
specific promoters can qualify as distinctive fea-
tures. Other features to be discussed are those
used in the classification of sigma 70 promoters
in Collado-Vides et al., 1991.
The L1 representation can be understood as
the theoretical transcription of the properties
used in the 'interpretation' of sequences of DNA
assigned by 'reading systems'. These 'reading
systems' correspond to different RNA poly-
merases with their associated set of regulatory
proteins and their respective interactions. Diffe-
rent sigma factors provide a different specifi-
city to the bacterial RNA core polymerase for re-
coguizing different DNA sequences as their res-
pective promoters (Helmann and Chamberlin,
1988). There is no question that information
that specifies which RNA polymerase is involved
in the transcription of a UGI is relevant to its
description, since all the promoters of the collec-
tion are identified as sigma 70 promoters.
The question is, where to locate this informa-
tion? There are two alternatives: either it is a
distinctive feature of promoter categories or it is
included within the general principles that
characterize sets of UGIs or 'languages of regu-
lation'. The latter proposal assumes separate
grammars for each set of UGIs of the different
'reading systems'. Compare, for instance, the
set of sigma 70 UGIs with that of sigma 54
UGIs. They have quite different properties in
terms of the mechanisms and distribution of
regulatory sites, and the assumptions on the
conditions for their regulation are also different
(Collado-Vides et al., 1991). The search for dif-
ferent grammars for each set seems a more ade-
quate approach than trying to integrate all the
principles and restrictions of occurrence of
sigma 70 and sigma 54 arrays into a single
grammar. Thus, considering that we are in-
vestigating the grammar of sigma 70 pro-
moters, there is no need to repeat each time that
promoters are sigma 70 promoters.
However, the striking differences between
sigma 70 and sigma 54 may not be the general
rule across different bacterial factors (Helmann
and Chamberlin, 1988), and if it is found conve-
nient to group into a single grammar UGIs with
different sigma factor specificity, then such pro-
perty would have to be indicated in each
promoter.
Incidentally, observe that the notion of 'lan-
guage' as the collection of all possible UGIs
grouped into a single theory or grammar is more
akin to different molecular systems of transcrip-
tion and regulation than to sets of UGIs specific
of particular species. Based on the similarity of
the transcription and regulation machinery,
sigma 70 UGIs of E. coli and Salmonella are
considered under similar principles. And, in a
similar way, sigma 54 UGIs of E. coli, Salmonel-
la and Klebsiella can be studied as part of a sin-
gle 'language' (Collado-Vides et al., 1991).
Thus, the species identification is not required
within the set of sigma 70 or within the set of
sigma 54 promoters. Elimination of species
identification assumes that either there are no
structural characteristics within the sequences
of promoters that would enable one to separate
the promoters of different species within a
sigma class or that if there are, they do not in-
terfere with the substitutability of promoters.
Let us return now to analyse whether 'lac',
'araC' or 'bioB' are distinctive features (see,

e.g., (10) in the accompanying paper). These
names identify specific promoters; in other
words, such symbols are shorthand representa-
tions of complete nucleotide sequences. Their
use in a complete representation seems to con-
tradict the aim of defining the minimal proper-
ties required to distinguish them. Certainly one
can expect that a smaller number of nucleotides
could suffice to distinguish any two promoters of
the collection of sigma 70 promoters. In addi-
tion, for the sake of regulation, such specific se-
quences are accidental, in the sense that there
are other sequences that can replace them
without significantly modifying the regulation
of the respective UGI.
We have then to widen the notion of promoter
'X' in order to include the set of in-
distinguishable sequences into a single distinc-
tive feature. For instance, a different notion of
promoter X, let us denote it by 'promoter X', can
be defined in such a way as to include all the se-
quences that have the same -10 and -35 se-
quences and the same distance in between them
as the native X promoter. As a first approxima-
tion, any sequence that satisfies these require-
ments can be substituted for the native
promoter X. However, even this extended no-
tion of 'promoter' is too specific to be considered
a distinctive feature. If promoters X and Y do
not differ significantly, there is no need to
associate to them a different distinctive feature.
All the promoter sequences that are in-
distinguishable in terms of regulation have to be
grouped into a single class. Such classes do not
depend exclusively on the conservation of those
specific nucleotides that enable us to distinguish
between 'promoters'. For instance, sigma 70 E.
coli promoters with different -35 domains can
have the same regulatory behaviour (see pro-
moters 14, 15 and 18 in Tsung et al., 1990). Con-
servation of promoter strength can be assumed
to be more important than conservation of speci-
fic sequences in the -10 and -35 domains.
There is no question that the distinction at
least between strong and weak promoters is rel-
evant for purposes of a regulatory description.
Negatively regulated promoters are usually
strong promoters, whereas positively regulated
107
promoters are usually weak promoters (De
Crombrugghe et al., 1982). An extreme illustra-
tion of this correlation is the example of an acti-
vator that can become a repressor by the
exclusive modification of the strength of the pro-
moter (Tsung et al., 1990). The properties of
strong (+) and weak (-) are closer to the notion
of a distinctive feature than the classes of 'pro-
moters' previously defined.
Promoter strength correlates with the se-
quence of the promoter. Most of the mutations
that make a sequence closer to the consensus
are up mutations, and most of those that make
the sequence less similar to the consensus are
down mutations (Hawley and McClure, 1983).
Thus, modifications either of the distance be-
tween the conserved domains, or of a nucleotide
in either the -10 or the -35 domain can give
equivalent results in terms of promoter
strength. Partitioning of promoters into dif-
ferent classes according to their strength does
not require to identify promoters in terms of the
specific sequences in the conserved -35 and -10
domains.
Observe that the 'strength' of promoters can
be decomposed into its two components, the
equilibrium dissociation constant Kd, and the ki-
netic constant of transition to open complex
(McClure, 1985). Features of strength of inter-
action can be decomposed into simpler parame-
ters until each mechanism of regulation is
described at the level of elementary chemical
steps (Eyring and Eyring, 1963). However, the
condition of simplicity of representation imposes
a limit to what is identified as a relevant feature,
preventing the overspecification of features.
The incorporation of these two parameters
within the set of distinctive features is justified
if they help to distinguish different classes of
promoters, where such classes are useful in a de-
scription that emphasizes regulatory properties
of UGIs.
A correlation has been found between consen-
sus in the -10 domain and binding of RNA poly-
merase, and consensus in the -35 domain and
isomerization kinetics (Studnicka, 1988). But if
these classes do not correlate with positive and
negative regulation, there is no motivation to
108
consider them as distinctive features. Recall
that activatable promoters can have a perfect
consensus -35 sequence (Tsung et al., 1990).
Based on the data and analyses available, there
are no reasons to consider the binding constant
and the isomerization constant as two separate
features. See also the discussion of affinity of
protein-DNA interaction in Section 3.1.
The number of classes of affinity for a certain
type of promoter should ideally reflect the num-
ber of biologically significant classes. For the
moment we assume two values, (+) for strong
and (-) for weak promoters, to be assigned to the
distinctive feature of 'affinity' or 'strength' of
promoters.
Strength is not the only feature required for a
satisfactory description of promoters. There are
other properties, which do not necessarily de-
pend on the internal structure of the sequences
involved in the binding of RNA polymerase and
which might need to be taken into account.
There is evidence indicating that downstream
sequences close to the promoters can play a role
in the efficiency of termination of transcription
of UGIs (Telesnitsky and Chamberlin, 1989).
When considering not only transcription initia-
tion but regulation of the UGI at different lev-
els, a 'termination' feature with two or more
values indicating the different conformations of
RNA polymerase should be included in more
complete grammatical models.
In the review of the database of sigma 70
UGIs it was useful to distinguish between 'multi-
ple', 'complex' and 'simple' promoters. Pro-
moters are called 'multiple' if their regulatory
region is connected to that of another promoter
and both are controlled by at least one common
element or transcribe the same gene. Promoters
that are either multiple or subject to several sys-
tems of regulation are called 'complex'. Finally,
those that are not complex are called simple pro-
moters (Collado-Vides et al., 1991). The proper-
ty 'multiple' with a (+) feature for multiple
promoters and a (-) feature for non-multiple pro-
moters could be proposed.
However, observe that these properties are
completely different from strength and termina-
tion properties, in the sense that they do not
impose restrictions on the substitutability of
promoters' sequences under the test of
regulatability. There is no reason to expect that
the nucleotide sequence of a simple or multiple
promoter would fail to replace another promoter
because of these properties. Recall that the dic-
tionary in the grammar contains the complete
sequence of promoters, irrespective of overlapp-
ing domains with other categories.
Alternatively, the character of simple, multi-
ple or complex promoters could be considered as
a property of complete UGIs and not of indivi-
dual Pr categories. Thus a UGI can be defined
as simple if it has a single promoter regulated by
a single system of regulation. A multiple UGI is
one with several promoters, and a UGI is com-
plex either when it is multiple or when its regu-
lation involves several systems of regulation.
The location of these properties as properties of
complete UGIs is based on the assumption,
previously mentioned, that there is no informa-
tion in the sequence of promoters that is associ-
ated with such properties. Furthermore, these
properties correlate with regulatory properties
of UGIs. It has been observed that duplicated re-
mote sites generally occur in arrays with multi-
ple promoters subject to multiple systems of
regulation (Collado-Vides et al., 1991).
In a similar way, supercoiling of the template
cannot usually be associated with one particular
molecular category. Together with the
character of multiple or simple UGIs, it has to be
incorporated at the level of complete UGIs. Cer-
tainly it has been observed that mechanisms of
regulation that involve binding sites of regula-
tory proteins located at a distance frequently
work better with supercoiled DNA than in linear
templates (Borowiec et al., 1987; Tobin and
Schleif, 1990; Richet and Raibaud, 1991).
The last feature of promoters that needs to be
discussed again is that of information on co-
ordinates. Briefly, recalling what has been
discussed in the previous paper, the reasons not
to include co-ordinates in promoters are the
following: (i) the precise location of all regula-
tory sites can be deduced from the distance of
remote sites and co-ordinates of proximal sites,
and (ii) the information on the boundaries of -65

to + 20 of the promoter is already used in the
principle of proximal precedence of sigma 70
UGIs.
In summary, specific names such as 'lac' and
'bioB' (or their complete nucleotide sequences)
do not satisfy the conditions to be considered
distinctive features of promoters. A strength or
affinity property with two or more values for
different degrees of strength is a distinctive pro-
perty of promoters. Other properties may also
be considered in more detailed descriptions of
promoters, such as a 'termination' property.
Properties of 'multiple' and 'subject to multiple
regulation' are not included as features of pro-
moters, assuming they do not affect the
substitutability of promoters. However, they
might well be located as properties of complete
UGIs, in the same way as the degree of super-
coiling of the DNA template. Finally, the co-
ordinates of individual promoters are not includ-
ed as distinctive features. The number of values
associated with each feature, as mentioned
before, should reflect the number of classes that
are biologically significant. We will assume two
classes of affinity, strong and weak promoters.
In the following we will address the question
of which are the distinctive features of regula-
tory sites with information on specificity of bind-
ing of regulatory proteins.
3. Distinctive features of regulatory sites
Operator and activator categories are the sites
where regulatory proteins bind to DNA and
then regulate gene expression by either preven-
ting or helping RNA polymerase to clear the
promoter and proceed into elongation of tran-
scription. In this section we will select the set of
properties of the Op and I categories that can
qualify as distinctive features. These properties
will include those that correspond to the Op/I
DNA target sites, those of their respective bind-
ing proteins, and those describing their interac-
tion. The set of distinctive features are
associated, in the dictionary, with the DNA se-
quences of these sites.
As a first approximation, one could think that
the set of these sites is divided into different mo-
109
lecular words, each one describing a site of in-
teraction with one protein. More precisely, each
DNA-protein specificity would correspond to a
group of molecular words, those that share that
specificity. However, since proteins contain
several other properties, this specificity is only
one among other properties that identify groups
of words. To name a protein means to refer to
a considerable number of properties that, to a
certain extent, can be modified independently.
For instance, when referring to a protein we are
referring to at least three different separable
domains of specificity: the domain of protein-
DNA interaction; the domain of recognition of
the allosteric signal, or that of the equivalent
covalent modification; and the domain that par-
ticipates in the formation of dimers and other
multimers with homologous proteins. Finally, in
the case of activators, as well as in some
repressors (Menon and Lee, 1990), another site
may be involved in the interaction with RNA
polymerase. As mentioned before, the L1
representation of 'deciphered' DNA sequences
has to include properties of regulatory proteins
(Collado-Vides, 1993, in press).
In the following section we will discuss each of
the properties that are important in the descrip-
tion of these regulatory sites.
3.1. Specificity of protein-DNA interaction
In representations like that of (10) of the pre-
vious paper, we used 'binds CRP' and 'binds
LacI' as features in proximal regulatory sites.
Following a reasoning similar to the discussion
on promoter identification, we can argue that
the description of the DNA binding domain of
the proteins can be reduced to only the elements
that are pertinent for the DNA-protein recogni-
tion. Thus, for instance, the recognition helix of
GalR and LacI differ only by three amino acids
(Lehming et al., 1987). The description of such
domains could therefore be reduced to a matrix
description indicating the positions with the
amino acids that are different. A simplified de-
scription for protein-DNA specificity depends on
the discovery of general rules for the different
types of protein domains for such interactions.
This is, however, a topic in itself as complex as
110
the search for general rules in the description of
UGIs (Lehming et al., 1990).
Since the dictionary contains the complete se-
quence of the DNA site, a 'protein-DNA' feature
bearing the specificity of that interaction only
requires to identify the protein domain. Such
domain can be identified by the name of the
protein. It should be clear, nonetheless, that con-
ceptually, such name corresponds to the minimal
set of amino acids used within a set of principles
that better describe the pertinent features of
protein-DNA interaction.
3.2. The affinity of the protein-DNA interaction
Depending on the specific nucleotide se-
quence, the strength or affinity of the binding of
a repressor protein to a DNA binding site can
vary by more than three orders of magnitude.
Substitutions within the class of all the se-
quences that recognize a single repressor are ex-
pected to affect regulation considerably.
For instance, the dissociation constant, Kd,
for LexA binding to recA is 2 nM, whereas the
Kd for binding to uvrB, lexA and clel is 20, 20
and 0.04 nM, respectively (Walker, 1987).
Similarly, an ideal lac operator binds eight times
stronger the lac repressor than the E. coli prox-
imal operator sequence (Simons et al., 1984).
Changes in the affinity of the lac operator
modify the promoter activity accordingly (Jobe
et al., 1974). A correlation between affinity and
deviation from homology has been observed in a
collection of CRP-binding sites (Berg and von
Hippel, 1988). Variations in the affinity of
repressors may establish a continuum of degree
of efficiency of repression, from constitutive to
normally regulated to excessively repressed
UGIs.
It is important to note that the range of affi-
nity we are talking about refers to specific bind-
ing of regulatory proteins to their DNA targets.
Sequences of DNA that can bind unspecifically
to proteins are ruled out from the grammatical
model by simply excluding them from the dic-
tionary. Similarly, putative binding sites for
which there is not sufficient evidence are also
excluded (see types of evidence in Collado-Vides
et al., 1991).
The fact that large differences exist in the
binding, for instance, of LexA to sites that occur
in nature indicates the importance of
distinguishing weak and strong sites. Thus,
several classes of affinity have to be considered.
Remote LacI sites are weak binding sites,
whereas the primary proximal site is the one
with the highest affinity (Gralla, 1989).
Finally, recall that the binding of a regulator
depends on the sequence of the DNA target site.
Within the levels of description so far available
in the grammar, there is no other alternative but
to identify the different variations, or mutant
operator sequences for a specific regulator, as
different molecular 'words'. Each sequence of a
set that binds the same target will only differ in
its affinity feature. In fact, it may well be that
more than one sequence determines the same
affinity feature.
In summary, these arguments support the
'affinity' as a distinctive feature of regulatory
sites. A feature with two values, high (+) and
low (-) affinity, or with more values, can be
used.
The affinity or strength of the protein-DNA
interaction can be described at different levels,
either at the level of an 'intrinsic affinity' or
'strength' parameter or using the equilibrium
constant of dissociation, Kd, of the protein-DNA
complex and the respective kinetic parameters
of association and dissociation; or, even more,
the elementary steps of the mechanism of reac-
tion could be used. Recall, however, that we are
identifying the level of description of this infor-
mation that better corresponds to what we
defined as a distinctive feature.
Consider, for instance, activator mechanisms.
The affinity of RNA polymerase binding or the
kinetic transition to open complex formation
and subsequent elongation can be modified
(McClure, 1985); increased escaping from
elongation is also documented (Menendez et al.,
1987).
A detailed description of these cases involves
several chemical parameters within the Pr cate-
gory, i.e. the equilibrium binding of the
promoter-RNA polymerase binding, the kinetic
constant of the transition of closed to open corn-

plex, and kinetic constants of the transition to
elongation. In order to conserve a homogeneous
level of description throughout the grammar, all
cases should include these parameters.
The importance of such information for the
understanding of regulatory mechanisms is not
being questioned. What we need to determine is
which information contributes to distinguishing
among different classes of substitutable pro-
moters. These classes would be justified if dif-
ferent classes of activators occurring with the
respective classes of promoters were found.
However, even if there are no studies on a large
number of proteins, evidence available indicates
that one cannot identify between 'the activator
protein that enhances binding of polymerase'
and 'the activator that enhances the transition
to open complex' as distinct classes of proteins.
Certainly the mechanistic properties of activa-
tors depend, not only on the protein but also on
the specific position of the site (Gaston et al.,
1990). In fact the same regulatory protein can
exert its activating effect by different
mechanisms (Igarashi et al., 1991; Richet et al.,
1991; Shevell and Walker, 1991). Similarly, the
repressibility of operator sites depends not only
on the intrinsic affinity for the repressor but
also on its precise location in relation to the pro-
moter (Lanzer and Bujard, 1988). And this time
we cannot easily include the positional compo-
nent by multiplying the number of entries in the
dictionary, since that would create entries with
identical sequences that only differ by their posi-
tional information. Such an approach would be
counterintuitive to the notion of a grammar as a
device that generates the diversity of UGIs with
the use of a combinatorial component (Collado-
Vides, 1993).
Based on the previous observations, we pro-
pose to consider a property that measures the
efficiency of the regulatory sites formed by two
components. One is the intrinsic affinity, a
distinctive feature included in the dictionary
characterizing the protein-DNA interaction. The
other property, which can be considered a sort
of 'correction' of the intrinsic affinity, depends
on the precise position of the sequence, and
therefore, is not included in the dictionary.
111
The theoretical reconstruction within a gram-
matical model of these properties of regulatory
sites is discussed in the grammatical model
presented in Collado-Vides, 1992.
3.3. The specificity of the sensor metabolite
Regulation of gene expression is dependent
on different physiological conditions that are
sensed by regulatory systems by means of an
interaction of small metabolites or chemical
modification of the regulatory proteins. Repres-
sion and depression of the lac system in E. coli
is dependent on physiological conditions that are
reflected in the intracellular concentration of
allolactose, the natural inducer that is recogniz-
ed by the LacI repressor. This allosteric site can
be modified without changing the repressor-
DNA interaction (Bourgeois and Jobe, 1970),
consequently affecting regulation.
Considering the importance of these signal
metabolites in regulation, it is intuitively attrac-
tive to include them as distinctive features. For
the sake of a first linguistic description, a 'signal
feature' with the name of the allosteric metabo-
lite or the covalent modification as its value
would suffice. Thus, LacI would have a signal
feature whose value is 'allolactose'. This value
indicates the specificity of the regulatory pro-
tein. An additional feature is required if we
want to distinguish the different protein confor-
mations associated with the binding and unbin-
ding of such signal molecules. It is important to
note that by specificity of the sensor metabolite
we refer to the allosteric site of binding of an in-
ducer, or binding of a corepressor or to the
chemical modification associated with a confor-
mational change of the regulatory protein.
The allosteric specificity is explicitly used in
an extended grammatical model that assigns dif-
ferent representations to alternative regulatory
states of UGIs. Such an extended model pro-
poses two basic representations for each UGI
(Collado-Vides, 1989 a). What is called the G
representation (for 'genome'), equivalent to
the so-called first linguistic representation, is
obtained by grammatical rules like those il-
lustrated in Collado-Vides (1992 (diagrams
2-5)). Subsequent E representations (for
112
'expression') can then be obtained that reflect
the alternative regulatory states of UGIs.
The transition from G to E representations is
achieved by transformational rules. These rules
modify the location of the regulatory protein
and its associated allosteric metabolite in the
linguistic representation of a UGI. In this way a
simplified description of the binding and unbin-
ding of regulatory proteins to their target sites
was obtained. In this extended model the sensor
metabolite was treated as a feature of the pro-
tein when bound to it and as a weak lexical ele-
ment when represented free in solution
(Collado-Vides, 1989).
The incorporation of an allosteric feature
within the set of distinctive features of regula-
tory sites will facilitate the establishing of a link
between the grammar of sigma 70 as conceived
here and an extended model that describes alter-
native states of regulation by means of transfor-
mational rules.
3.$. The domain of homologous protein-protein
interactions
The specificity of domains of regulatory pro-
teins determines the interactions among
homologous regulatory proteins that participate
in systems of regulation with multiple sites.
These interactions can play an important role in
repressing mechanisms, for instance involving
looping of the intervening DNA. In other cases
with duplicated sites more closely located to
each other, such protein domains mediate co-
operative interactions. Modification of such do-
mains can impair a mechanism of regulation
even if the protein-DNA interaction is not al-
tered (Haber and Adhya, 1988; Menon and Lee,
1990). This property is then necessary to
achieve a description of a system of regulation.
There is no doubt that properties of this type
will have to be analysed in much more detail
when considering eukaryotic systems of regula-
tion, where additional distinctions will be re-
quired (Ptashne, 1988). In fact one can consider
an affinity feature associated with each dif-
ferent specificity property of regulatory pro-
teins. Although this is reasonable in principle
(Bourgeois and Jobe, 1970), there is not a suffi-
cient number of different cases of regulation in
sigma 70 to justify such additional affinity
feature.
3.5. The stab~ form of a regulatory protein in
solution
The predominant multimeric nature of regula-
tory proteins in solution varies depending on the
protein. Thus, for instance, the lambda
repressor is a dimer (Ptashne, 1986), Lacl
repressor is a tetramer (Riggs et al., 1970), and
AraC is a dimer (Wilcox and Meuris, 1976),
whereas DeoR is an octamer (Mortensen et al.,
1989). In Table 1 we have collected several pro-
perties of the regulatory proteins, including the
multimeric nature of the protein, the size of the
binding site, and the type of repeat.
The multimeric nature of the protein is impor-
tant for understanding mechanisms of regula-
tion involving bound DNA between multiple
homologous sites. Certainly the looping forma-
tion by a protein that binds as a tetramer in-
volves only two specific recognition events, the
binding of the protein to one site and the subse-
quent binding of the other DNA site to the
bound protein. In the case of a dimer, the loop
formation involves, in principle, three recogni-
tion events, the separate binding of a dimer to
each DNA site together with the recognition be-
tween the two bound proteins.
Observe, however, that a dimer of AraC can
form a loop of DNA, which means that a single
monomer binds to each DNA site (Lobell and
Schleif, 1990). But, unlike DeoR, GalR, or LacI,
AraC is an activator whose site is not an invert-
ed repeat. Furthermore, the size of a direct re-
peat of AraC is exceptionally large: 17 base
pairs, compared with the usual 10 bp size of
direct repeats of other activators (see Table I).
These observations suggest that AraC
stoichiometry in looping formation is more an
exception than a usual case.
One would expect that the larger multimeric
proteins facilitate looping of DNA, allowing for
larger distances between the operator sites.
Observe that the most distant operator sites of
the collection are those involved in looping for-
mation with DeoR, which is an octamer
 113

(Amouyal et al., 1989). Incorporation of the
multimeric stable state of proteins as a distinc-
tive feature depends on whether it proves useful
in identifying classes of regulatory proteins with
similar restrictions in the occurrence of remote
sites.
3.6. Orientation of sites; internal structure:
direct and inverted repeats and asymmetric
sites
An entry in the dictionary associates a set of
distinctive features with a short sequence of
DNA. This sequence is oriented, indicating

Table I. Multimeric state of regulatory proteins and size of their binding sites

Protein Multimer Size Orientation References

Ada 1 12 a Asymmetric Sakumi and Sekiguchi, 1989; Shevell and

Walker, 1991
AraC 2 17b Direct Lee et al., 1987; Wilcox and Meuris, 1976
ArgR 6 16 Inverted Cunin et al., 1983; Lim et al., 1987
BioB 2 40 Inverted Otsuka and Abelson, 1978
CRP 2 19 Inverted Busby, 1986
CysB 4 36 - 46 a a Ostrowski and Kredich, 1991
CytR n.d.C 40a n.d.C Gerlach et al., 1991; S~gaard-Andersen et
al., 1991
DeoR 8 16 Inverted Amouyal et al., 1989; Mortensen et al., 1989
DnaA 1a 95 Direct a Wang and Kagun, 1989
FNR n.d. c 22 Inverted Eiglmeir et al., 1989
Fur 2a 19 Inverted de Lorenzo et al., 1987
GalR 2 17 Inverted Majumdar and Adhya, 1987
GlpR 4 20 Inverted Ye and Larson, 1988
IcIR n.d.C 34 Inverted Cortay et al., 1991
IlvY n.d.C 26 Inverted Wek and Hatfield, 1988
LacI 4 20 Inverted Gilbert and Miiller-Hill, 1966; Riggs et al.,
1970
LexA 2 20 Inverted Little et al., 1981
MalT 1 10 b Direct Vidal-Ingigliardi et al., 1991
MetJ 2 85 Direct Phillips et al., 1989
MetR n.d. c 24 Inverted a Urbanowski and Stauffer, 1989
NR(I) 2 15 Inverted Ueno-Nishio et al., 1984; Reitzer and
Magasanik, 1983
OmpR 1,2a 10b Direct Maeda and Mizuno, 1988, 1990
OxyR n.d. c >45 _a Tartaglia et al., 1989
PboB n.d. c 17 b'a Direct Makino et al., 1986
PifC n.d.C 20 Inverted Kennedy et al., 1988
Purr 1- 2a 16 Inverted Rolfes and Zalkin, 1990
PutA 2 27 Inverted Ostrovsky et al., 1991
RafR n.d. c 18 Inverted Aslanidis and Schmitt, 1990
RhaR 2 20 Inverted Tobin and Schleif, 1990
TetR 2 25 Inverted Takahashi et al., 1986
TrpR 2 27 Inverted Klig et al., 1988
TyrR n.d. c 22 Inverted Chye and Pittard, 1987

a Not a precisely defined property.

b Direct repeat or 'box' size.
c n.d., not determined.
114
which is the 5' end and which is the 3' end. Cer-
tainly some regulatory proteins exert their
effect only in a specific orientation in relation to
the promoter.
However, in some cases the inversion in the
orientation of a complete binding site conserves
the regulatory properties of the bound protein.
Although mostly common in enhancers, some
bacterial sigma 70 and sigma 54 activators are
also orientation-independent (De Crombrugghe
et al., 1982; Maeda and Mizuno, 1988; Reitzer
and Magasanik, 1986). The addition of a feature
indicating orientation independence (+) or ori-
entation dependence (-) associated with regula-
tory sites gives a more economic representation
than the alternative solution of considering each
oriented sequence as a different molecular
'word' with all the properties repeated.
This orientation feature must not be confused
with an arrow feature used in a grammatical
derivation that enables a single representation of
proximally located multiple promoters. In these
representations that can also include divergent
promoters, an arrow was used on promoters to
indicate the direction of transcription and on Op
and I sites to indicate the direction of promoters
that are subject to their regulatory effect
(Collado-Vides, 1991). These arrow features, how-
ever, are not necessary in descriptions analysed
here restricted to a single promoter.
Regulatory proteins usually bind as dimers to
a single Op or I site. Symmetry properties are
therefore common in these DNA sequences,
with sites usually having direct or inverted re-
peats, although cases with no repeating units
might also exist (see Table 1). Frequently Op
sites are formed by inverted repeats, and activa-
tor proteins bind to sites formed by direct re-
peats, although there are several regulatory
proteins that do not follow that correlation, as
can be observed in Table 1. In some few cases,
direct repeats occur as separated half-sites ac-
companying a pair of direct repeats that form
either an Op or an I site (Collado-Vides, 1993).
These properties are not expected to contribute
to the identification of classes of substitutable
elements. Recall that the grammatical rules will
permit a combinatorial description of UGIs
based on their regulatory properties, which de-
pend basically on the categorial Op/I identifica-
tion of sites. The distinction between direct and
inverted repeats is a property internal to molec-
ular words, which does not directly determine
their substitutability.
It has been proposed that the distinction
between direct and inverted repeat may be re-
lated to the evolutionary origin of regulatory pro-
teins (Raibaud, 1989). Thus, they may be justified
as distinctive features if in future developments
of the linguistic theory a component containing
evolutionary information is organised.
3.7. Positional restrictions and phase restric-
tions
Finally, we have to discuss information on
position of sites. In the accompanying paper we
have already shown that the precise position of
proximal sites is a distinctive feature. Here we
will discuss alternative ways to represent the
position of remote sites.
Recall that remote sites cover the range from
-900 for DeoR to + 400 for LacI. The positions
of duplicated homologous operators and activa-
tor sites have been analysed in detail elsewhere
(Collado-Vides and Claverie-Martin, unpublish-
ed). The analysis supports a general rule in the
architecture of arrays of duplicated homologous
operators allowing the proteins to bind on the
same face of the helix.
A simple way to capture this general rule in
the grammatical description is to indicate the re-
lative distance of remote operator sites in rela-
tion to the proximal site using the number of
helix turn repeats as a measuring unit. Recall,
however, that the position of remote sites is in-
dicated always in relation to the proximal refer-
ence site. If phasing information is to be used
also for position, it is restricted to distance rela-
tive to the proximal site. It is possible to con-
sider a set of homologous duplicated sites where
not all of them are in phase, particularly in rela-
tion to the proximal site. The malK promoter il-
lustrates in fact a case where the proximal site
is not in phase, while other sites are in phase
(Raibaud et al., 1989).
Thus, the most reasonable description is that

position information of remote sites is indicated
by its relative distance to the proximal site, as
has been discussed in the previous paper. In ad-
dition, sets of sites that co-operate via protein-
protein interactions will have a phasing feature
with indication of their relative distance
measured in helix turns. Proximal or distal sites
can have this feature, which gives an explicit
identification of those sites supporting either co-
operative interactions or DNA looping.
Thus, we conserve the distinction between
proximal and remote sites by means of the co-
ordinate and distance features, as proposed in
the previous paper. Additionally, a phasing fea-
ture, indicating the distance measured in helix
turns between any two sites, identifies those
sites supporting co-operative protein-protein in-
teractions and/or interactions enabling a DNA
loop between them.
3.8. Recapitulation of Op and I distinctive
features
In summary, we started analysing the
specificity of the protein-DNA interaction of
regulatory proteins searching for an economic
way to describe the property 'binds X'. How-
ever, we saw that there are many more distinc-
tire features that naturally belong to 0p and I
categories. These include three domains of
specificity: the specificity of the protein-DNA in-
teraction, the specificity of the sensor metabo-
lite or domain of allosteric or chemical
modification of the protein, and the specificity of
the domains that determine protein-protein in-
teractions that participate in systems of regula-
tion with multiple sites. The set of features
included in a proximal site, such as for instance
the CRP binding site in the structure (12) of the
previous paper, can be stipulated as:
-- I --
cj = -60
Aft: (+)
sensor cAMP
m=2 (1)
p-p: CRP dimers
DNA-binding: CRP sites
__ orientation: (+) _ ability restrictions.
115
where c indicates the co-ordinates with -60 the
position of the central nucleotide. The j subindex
is used to differentiate this site from those bind-
ing the LacI protein, which have an i sub-index.
The size of sites is considered a property associ-
ated with the protein, therefore it is not explicit-
ly included in (1). The dictionary contains such
'word' properties associated with the different
proteins. Aft, the affinity feature, can be assum-
ed to take two values for high (+) or low (-) affi-
nity. The 'sensor' feature indicates the
specificity of the metabolite that induces the al-
losteric modification responsible for alternative
regulatory states of the protein, m is the feature
for the multimeric state of the protein bound to
DNA, the value of 2 indicating dimers. 'p-p' in-
dicates the protein-protein specificity. In the ab-
sence of a better name, 'CRP dimers' is used to
refer to the specificity of the domain of CRP
proteins that is involved in homologous protein-
protein interactions. It is misleading in the sense
that a protein groups together three different
specificities, of which 'CRP dimers' is only one,
as discussed before. The individual identification
of these properties reflects the assumption that
such specificity determinants can in principle be
altered independently.
Finally, an orientation feature indicates that
inverted CRP sites can activate transcription.
Similar matrices can be used for other proximal
sites.
In the case of remote sites, a distance d fea-
ture conveys the positional information with the
number of bases that separates it from the prox-
imal referential site. The index indicates that
these sites share the same specificities as the
proximal referential site with the same index.
Therefore, these shared features are not includ-
ed in remote sites. Additionally, proximal and
remote sites have a phase feature indicating a
distance measured in helix turns when they are
involved in co-operative interactions or in DNA
looping.
Indication of symmetry properties of sites is
excluded, because it does not help to identify
classes of sites subject to uniform substitut-
116
Regulator Promoter

Ada ada
/cii_52/+f~,l
Ada) ~ )

Ada alkA
Ada )

AraC,CRP araBAD
~ph=19.0) eL6,1` /
op
AraC,CRP araC di=+1361
ph=13.0)

AraC araE
AraC ) :'43/,71
/dJci~ 6J + ci--D~-64/+

o0
ArgR argCBH (ci=+19/
/ArgR) ~ph=2.0)

ArgR argE
ArgR ) ph=2.0)

ArgR argF
/ ArgR ) )h=2.0)

ArgR a rgl + |ci=-231 + | ci=-2

~,ArgR ) (,ph=2.0

~r/+ ciOP29/+ ci_-Ol~_7

ArgR argR pl
ArgR) 9h=2.1

ArgR carAB p2 + (ci=+14/

(,ArgR) (,ph=2.1)

BioB bioA
/ BioB )
 f

~.~.~ +
,T ,7
+
J
"4-
+ +
-I- 4-
1- ÷~ ~,~o
b~
r ~ r
~o
~,.- J

~ J
+
 ~J
oo
0 0
>

t.~

f £b r ~ r ~ L.O ,.-4
~ '0
&'= ~'0
+ .&. + -t-
& +
,-.4
J
+ "4- ~ J \ J ~. J 4- +
r r ,_~ + "~'o 4- +
.
f ~ f ~
,<N'O
~ J
+
+ +
f -x
+
+
II
a? ,7
+
'..
b, .J
4- + +
'T? t~ -. j
p +
t~ M ~

.~.

b,
+
r ~

4-
 119

FNR,NarL narG
dj =_I159#)+/dj=-36#/+/ci=-41/+
I I ? r/
t NarL) tFNR ) t )

FNR,NarL nirB
NarL )

Fur cir p l ~ r)+/ci=O-P32) + IciOP26

~ Fur

Fur cir p2 / Pr +/ci=Off21 +/ciO-Pl31

t Fur )

Fur fhuA
~ Fur

Fur iucA p l
t,ph=2.2) ~ Fur )

GalR,CRP gal p l J~2~/~'5 + + Ici__OP_61+~i_-+1o41

Op
t Gain t ph=10.0)

GalR,CRP gal p2 ~r) +/ciOP56/ + (cj~6) + di=+104

O19
t. OalR ) ~ph=lO.O

GIpR,CRP glpO fci=6~l+(~l+~c~'/ +Ic~:+~01

I r
Op
CRP ) ~ ) ~GIpR) ~.ph=l.8)
Pr~ ( Op
IclR aceBAK
I / + I ci=-40#
) ~ Icla

IlvY ilvC pCiI64 +/ciI-31)+ ~r 1

h=3.1 t IlvY J

IlvY i lv Y
{P'
( IlvY ) tph=3.1)
120

LacI, CRP lac +

(i/?)
~:~o+ + ~c~9~+r~i:+,o~)
oo
t,Lacl) /ph=8.9 )

LexA cloDF14
) CLexn)

LexA, CRP colE1 pl

ph=4.2 LexA) t,ph=1.6

LexA lexA
fr/+/c,°:,o/ oo
/LexA ) ~ph=2.0)

er ,iOPl/
LexA recA
LexA )

LexA ssb
t LexA )

LexA sulA / /LexA)

LexA uvrA
/ LexA )

LexA uvrB p2
/P'/+
LexA )

Pr ( Op
LexA uvrD 1 + / ci=+11
) ~LexA

( 1/2I ") I I I I I "~ ( v q

MalT, CRP malE ?:,~9j +/di=-160/+~dj=-95 /+ dj=-61)+fdj=-32)+ ci=-44|+| /
~ph=15.3)lph=10.8 ) ph=2.8) ~ CRP ) MalT) t. )

MalT, CRP malK |ci=-681+|ci=-37.5|

t.ph=15.3) t.ph=10.8) t,ph=2.8) t CRP ) ~MalX) t )

MalT malPQ ci---66|+|ci=-36.51 +

MalT) t, )
 121
MetJ metA pl r/+rc,:~.~] o0
+ ci=+20.5
t ) ~ MetJ )

MetJ metB ci=-31.5

Pr']+ ([d ]I/2Op"~ Op Op

MetJ metJ
J i=-75.5) t, ) t MetJ )

MetJ metF + (ci=+4,5]+ Op

t. MetJ )

MetR, MetJ metE | 1+ Ici=+6]'~ ci=+17|

t,MetR) t, ) t, ) (, MetJ )

MetR metR ci=+%4]

MetR )

MetR metH
iI-56] + ~ r]
etR )

NR(I), CRP glnA pl ~=g,+ + c?t+[ °,% ]

NR(I)) t. ph=3.2)
r Op
NR(I) glnL ~]+(c,:_1]
l ) /NR(I))

iI-40] ~ci=I-66 ] + (ciI-46] + (Pr)

OmpR ompC
I:h=3.8) (ph=l.9) t.OmpC)

Op I
OmpR ompF [di=-a22]cfdi=-50]+ fdi--I-40 +(ciI-30
{,ph=31.5) {,oh=4.8) (ph=3.8 t,ph=Z.9 (OmpC

OxyR aapC
OxyR )

OxyR katG
OxyR )

OxyR ahpC Il+rciI=-/oxy

 J
+
f
~:~+
J
+ 0 il
+
f f ,x J
+
tf3 f -x
,i
.1~ ~ . .
+ +
+
J
©ll~. ©.~ . . f o .,,
f
f
+
.-, J
'Fa ~ ~ J ~ J
~ J
+ + + + +
+ + + +
~e~, o rn 0 C "
T. "
~ J
~ J
g
 q

f r ~ r ~ r ~ r
r ~
= ~';'o
,. 2, + + +
+ + + +
+

+ ~ II ~
+ + .o ~o ~,7o ,,o ~'7o
,,~ II 0
r " xh
J
+ + +
,7
f

~ II 0 ii II O ~.~ ~', +
~ + ~ ~ ' 0 J
+
~ J

+
g,7o
+

+ ~.

+
f c) ~'

>E
124

TyrR aroL /Pr) ( Op Op

t, ) ~,ph=5.4 ~ph=2.0) / T y r R )

TyrR aroP /+ Ici:÷41i ÷ [di=+%3

) (TyrR) ~,ph=2.1

TyrR tyrB
~TyrR ) ~.ph=2.1)

TyrR tyrP
kph=2,1) / T y r R )

TyrR tyrR
/ TyrR )

Fig. 1. A distinctive representation of sigma 70 UGIs. This linguistic representation of the range of transcription initiation
of sigma 70 promoters results from the application of the proposals discussed throughout this and the accompanying paper.
Proximal sites have a coordinate c feature indicating the position of their central nucleotide. Remote sites have a distance d
feature indicating the number of center-to-center bases relative to the proximal referential site. For size of sites see Table I.
The referential site is the one that bears the name of the regulator. Co-indexation identifies the specificity of remote sites. A
phasing (ph) feature indicates the number of helix turns that separate homologous sites from the referential site. Phasing is
always in relation to the site of reference for co-indexation or specificity. The # symbol is associated with not precisely defined
properties. For additional information see Fig. 1 of accompanying paper.

3.9. A complex 'binds X' feature
We have decomposed the property 'binds X',
where X is a protein, into the set of properties
illustrated for a CRP site in Fig. 1. A particular
characteristic that applies to bacterial regula-
tory proteins can be made explicit by in-
tegrating this set of distinctive features into a
complex feature.
The grouping of several features into a com-
plex 'binds X' feature can reflect the fact that
even though the features can be modified in-
dependently, they are all properties associated
with a single protein. This contrasts with
mechanisms of regulation in eukaryotes, which
frequently involve interactions among several
proteins, each one containing different domains
of specificity that are all required together to ac-
tivate a promoter. This grouping of features into
a single complex can then be considered part of
the set of principles of the grammar of sigma 70
promoters, as well as of grammars of other pro-
karyotic promoters. In this way an important
difference among systems of regulation is em-
phasized.
Thus, a property 'binds X', where X is a pro-
tein, can substitute for several properties direct-
ly dependent on the protein. Those properties
that are not associated with a particular protein
are excluded from this grouping, such as the
affinity of the binding site and position and
phasing information. The co-indexing of remote
sites will then refer to homology of the set of
properties associated with a particular protein.
With this proposal we finish the analysis of
distinctive features of regulatory sites. The ap-
plication of the principle of precedence, as well
as the identification of the distinctive features of
Pr, Op and I categories, enables us to transcribe

the arrays of sigma 70 UGIs collected in Fig. 1
of the previous paper into their corresponding
linguistic description, shown here in Fig. 1. This
diagram summarizes the distinctive features
that have been identified throughout these two
papers.
4. Discussion
The results that Fig. 1 represent have been
obtained by studying all the properties that we
know of as relevant to the regulatability of
sigma 70 UGIs. For instance, detailed parame-
ters of mechanism of reaction have been exclud-
ed, since they do not seem to contribute to the
identification of classes of substitutable ele-
ments. These two papers illustrate that the
problem of finding the best linguistic repre-
sentation, following explicit criteria, can give
concrete results. Recall, for instance, the
representation of positional information as
either an independent category or as a feature
of regulatory sites. The use of a small number of
criteria in the selection of properties of quite dif-
ferent nature represents by itself a descriptive
challenge, as these papers illustrate. The distinc-
tive features obtained are the elements of a the-
oretical characterization of a particular 'reading
system'. When dealing with different 'reading
systems', a similar analysis would be required.
Among the similarities between the transition
of an acoustic to a phonological description in
the study of natural language, and the transition
of a description of UGIs to an L1 linguistic
description, we have the following: (a) a
phonological description uses elements that
characterize natural language as a system; (b) it
is a transcription that presents 'raw' informa-
tion in a form suitable for linguistic analysis; (c)
the criteria for defining distinctive features are
in a way the same as those used here. It is
no surprise that these similarities exist, because
of the similarity in methods used in the
phonological study of natural language (Chom-
sky and Halle, 1968) and in the study of distinc-
tive features of sigma 70 UGIs.
On the other hand it is also no surprise to see
important differences, since the object of each
125
Study is different. The dictionary of the gram-
mar associates with each 'word' a list of perti-
nent selected properties, the sequence of DNA,
'raw information', being one of them. There is
nothing equivalent, in a linguistic theory of nat-
ural language, to a dictionary that groups acous-
tic descriptions and their associated phonologi-
cal properties. An equivalent treatment of mo-
lecular data would involve the definition of mo-
lecular 'words' using only distinctive features.
Following this approach, only two promoter
'words' would be present in the dictionary, that
of 'promoters with high affinity' and that of
'promoters with low affinity' (see Section 2).
The differences within these classes would be
considered 'negligible variants'. However, the
incorporation into the dictionary of the different
sequences of Prs, Ops and Is makes more sense
in the search for a theory of gene regulation
with a combinatorial component (Collado-Vides,
1993, in press).
The analysis presented here assumes that
there is a finite set of features that define the
best representation of a particular 'reading sys-
tem'. However, since we cannot rule out the
discovery in the future of new correlations be-
tween relevant properties of such regulatory in-
terpretation of UGIs, the set of features here
identified may not be the minimal one. Unknown
properties yet to be discovered may satisfy the
criteria of distinctive features. In some cases we
were able to select distinctive features although
their specific values associated are not yet defin-
ed. This is a consequence of a formalization of a
data-base where each case is not equally well
known. Certainly the proposals presented here
might be modified as our understanding of gene
regulation increases in the future.
The construction of a grammatical theory of
gene regulation depends to a considerable ex-
tent on the comparison and selection of alterna-
tive ways to represent the data, from a single
property such as the distance between
categories to complete alternative grammatical
models. In fact the study of natural language us-
ing generative grammars is a discipline of em-
pirical investigation where one could say that
our progress in understanding is associated with
126
novel proposals on representations or with novel
relations between different representations.
Recall that the theory of linguistic structure is
'essentially, the abstract study of levels of
representation' (Chomsky, 1955).
The selection of good representations is im-
portant not only within linguistic theory or ap-
proaches to artificial intelligence but also in
natural sciences. This is illustrated, for instance,
by the selection from a large number of physical
properties of those that are the most important
for determining protein structure and conforma-
tion (Kidera et al., 1985).
Grammatical models of gene regulation may
represent a useful contribution to the computer
scientist when dealing with the processing of
large amounts of deciphered information con-
cerning the regulation of gene expression.
The linguistic formalization of gene regulation
constitutes a set of ordered results that include
the identification of the smallest elements of
productive substitutions, the identification of
distinctive features, the construction of the com-
ponent of rewriting rules, and their integration
into a grammatical model.
A modification in any of these steps can have
important consequences in other components of
this integrative linguistic formalization. This
reconstructive effort at formalization should be
evaluated in terms of its capacity to integrate
large amounts of information and in t e r m s of its
predictive power (Collado-Vides, 1992).
Acknowledgments
The author acknowledges several fruitful
discussions throughout the elaboration of this
work with Prof. Boris Magasanik. This work
was begun when the author was a postdoctoral
fellow in his laboratory in the D e p a r t m e n t of
Biology of the Massachusetts Institute of Tech-
nology. More recently the author has been sup-
ported by a Guggenheim Fellowship.
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