Positional Preferences of Polypurine/Polypyrimidine Tracts in Saccharomyces cerevisiae Genome: Implications for cis Regulation of Gene Expression

The complete genome of the baker's yeast S. cerevisiae was analyzed for the presence of polypurine/polypyrimidine (poly[pu/py]) repeats and their occurrences were classified on the basis of their location within and outside open reading frames (ORFs). The analysis reveals that such sequence motifs are present abundantly both in coding as well as noncoding regions. Clear positional preferences are seen when these tracts occur in noncoding regions. These motifs appear to occur predominantly at a unit nucleosomal length both upstream and downstream of ORFs. Moreover, there is a biased distribution of polypurines in the coding strands when these motifs occur within open reading frames. The significance of the biased distribution is discussed with reference to the occurrence of these motifs in other known mRNA sequences and expressed sequence tags. A model for cis regulation of gene expression is proposed based on the ability of these motifs to form an intermolecular triple helix structure when present within the coding region and/or to modulate nucleosome positioning via enhanced histone affinity when present outside coding regions.

Conformational preferences of α-functionalised keten-S,N-acetals: Potential role of SO and SS interactions in solution

PMR spectra of carbonyl compounds 2a-k reveal significant variations in the population of E and Z isomers on changing the solvent from CDCl3 to DMSO-d6. In non-polar media, the intramolecular N-H…. O hydrogen bonded form is exclusively observed. In DMSO-d6, the alternative Z form is also populated. A similar conformational switch is also noted in the corresponding thiones. Different interpretations are critically analysed. The most consistent explanation is suggested to involvean interplay of N-H….X hydrogen bonding and S…X attractive interaction (X = O,S) in these systems. Ab initio calculations support this interpretation.

Performance of established native seedlings in relation to invasive Lantana camara, rainfall and species' habitat preferences in a seasonally dry tropical forest

Native species' response to the presence of invasive species is context specific. This response cannot be studied in isolation from the prevailing environmental stresses in invaded habitats such as seasonal drought. We investigated the combined effects of an invasive shrub Lantana camara L. (lantana), seasonal rainfall and species' microsite preferences on the growth and survival of 1,105 naturally established seedlings of native trees and shrubs in a seasonally dry tropical forest. Individuals were followed from April 2008 to February 2010, and growth and survival measured in relation to lantana density, seasonality of rainfall and species characteristics in a 50-ha permanent forest plot located in Mudumalai, southern India. We used a mixed effects modelling approach to examine seedling growth and generalized linear models to examine seedling survival. The overall relative height growth rate of established seedlings was found to be very low irrespective of the presence or absence of dense lantana. 22-month growth rate of dry forest species was lower under dense lantana while moist forest species were not affected by the presence of lantana thickets. 4-month growth rates of all species increased with increasing inter-census rainfall. Community results may be influenced by responses of the most abundant species, Catunaregam spinosa, whose growth rates were always lower under dense lantana. Overall seedling survival was high, increased with increasing rainfall and was higher for species with dry forest preference than for species with moist forest preference. The high survival rates of naturally established seedlings combined with their basal sprouting ability in this forest could enable the persistence of woody species in the face of invasive species.

Tethering preferences of domain families co-occurring in multi-domain proteins

Genomic data of several organisms have revealed the presence of a vast repertoire of multi-domain proteins. The role played by individual domains in a multi-domain protein has a profound influence on the overall function of the protein. In the present analysis an attempt has been made to better understand the tethering preferences of domain families that occur in multi-domain proteins. The analysis has been carried out on an exhaustive dataset of 2 961 898 sequences of proteins from 930 organisms, where 741 274 proteins are comprised of at least two domain families. For every domain family, the number of other domain families with which it co-occurs within a protein in this dataset has been enumerated and is referred to as the tethering number of the domain family. It was found that, in the general dataset, the AAA ATPase family and the family of Ser/Thr kinases have the highest tethering numbers of 450 and 444 respectively. Further analysis reveals significant correlation between the number of members in a family and its tethering number. Positive correlation was also observed for the extent of a sequence and functional diversity within a family and the tethering numbers of domain families. Domain families that are present ubiquitously in diverse organisms tend to have large tethering numbers, while organism/kingdom-specific families have low tethering numbers. Thus, the analysis uncovers how domain families recombine and evolve to give rise to multi-domain proteins.

NON-GLYCINE RESIDUES IN THE DISALLOWED REGIONS OF THE RAMACHANDRAN MAP AND THEIR NEIGHBORHOOD PREFERENCES

The allowed and the ``disallowed'' regions in the celebrated Ramachandran map (phi-psi] map) was elegantly deduced by Ramachandran, Ramakrishnan and Sasisekharan even before the protein crystal structures became available. This powerful map was derived based on rigid geometry of the peptide group and later several investigations on protein crystal structures reported the occurrence of a small fraction of the phi-psi] torsion angles in the disallowed region. The question is what factors make these residues adopt disallowed conformations? Is it driven by the necessity to maintain the overall topology or is it associated with function or is it just that the disallowed conformations are extreme limits of the allowed conformations? Today, with the availability of a large number of high resolution crystal structures, we have revisited this problem. Apart from validating some of the earlier findings such as residue propensities, preferred location in the secondary structure, we have explored their spatial neighborhood preferences using the protein structure network PSN] approach developed in our lab. Finally, the structural and functional implications of the disallowed conformations are examined.

Sequence and conformational preferences at termini of alpha-helices in membrane proteins: Role of the helix environment

-helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These -helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze -helices in a high-resolution dataset of integral -helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. Proteins 2014; 82:3420-3436. (c) 2014 Wiley Periodicals, Inc.

A comparison of the molecular orbital (ab initio, CNDO and EHT) methods applied to the conformational study of thiocarbonohydrazide in its basic and diprotonated forms

Conformational preferences of thiocarbonohydrazide (H2NNHCSNHNH2) in its basic and N,N′-diprotonated forms are examined by calculating the barrier to internal rotation around the C---N bonds, using the theoretical LCAO—MO (ab initio and semiempirical CNDO and EHT) methods. The calculated and experimental results are compared with each other and also with values for N,N′-dimethylthiourea which is isoelectronic with thiocarbonohydrazide. The suitability of these methods for studying rotational isomerism seems suspect when lone pair interactions are present.

Modeling the role of competition and cooperation in the evolution of katydid acoustic synchrony

The precise timing of individual signals in response to those of signaling neighbors is seen in many animal species. Synchrony is the most striking of the resultant timing patterns. One of the best examples of acoustic synchrony is in katydid choruses where males produce chirps with a high degree of temporal overlap. Cooperative hypotheses that speculate on the evolutionary origins of acousti synchrony include the preservation of the species-specific call pattern, reduced predation risks, and increased call intensity. An alternative suggestion is that synchrony evolved as an epiphenomenon of competition between males in response to a female preference for chirps that lead other chirps. Previous models investigating the evolutionary origins of synchrony focused only on intrasexual competitive interactions. We investigated both competitive and cooperative hypotheses for the evolution of synchrony in the katydid Mecopoda ``Chirper'' using physiologically and ecologically realistic simulation models incorporating the natural variation in call features, ecology, female preferences, and spacing patterns, specifically aggregation. We found that although a female preference for leading chirps enables synchronous males to have some selective advantage, it is the female preference for the increased intensity of aggregations of synchronous males that enables synchrony to evolve as an evolutionarily stable strategy.

Cyclic Peptide Disulfides - Solution And Solid-State Conformation Of Boc-Cys-Pro-Aib-Cys-S-S-Bridge-Nhme,A Disulfide-Bridged Peptide Helix

The solution and solid-state conformations of the peptide disulfide Boc-Cys-Pro-Aib-Cys-NHMe have been determined by NMR spectroscopy and X-ray diffraction. The Cys(4) and methylamide NH groups are solvent shielded in CDCI3 and (CD,),SO, suggesting their involvement in intramolecular hydrogen bonding. On the basis of known stereochemical preferences of Pro and Aib residues, a consecutive @-turn structure is favored in solution. X-ray diffraction analysis reveals a highly folded 310 helical conformation for the peptide, with the S-S bridge lying approximately parallel to the helix axis, linking residues 1 and 4. The backbone conformational angles are Cys(1) 4 = -121.1', $ = 65.6"; Pro(2) 4 = -58.9', 4 = -34.0'; Aib(3) 4 = -61.8', $ = -17.9'; Cys(4) 4 = -70.5', $ = -18.6'. Two intramolecular hydrogen bonds are observed between Cys(1) CO--HN Cys(4) and Pro(2) CO--HNMe. The disulfide bond has a right-handed chirality, with a dihedral angle (xss) of 82'.

Proline-containing β-turns in peptides and proteins: Analysis of structural data on globular proteins

Tetrapeptide sequences of the type Z-Pro-Y-X were obtained from the crystal structure data on 34 globular proteins, and used in an analysis of the positional preferences of the individual amino acid residues in the β-turn conformation. The effect of fixing proline as the second position residue in the tetrapeptide sequence was studied by comparing the data obtained on the positional preferences with the corresponding data obtained by Chou and Fasman using the Z-R-Y-X sequence, where no particular residue was fixed in any of the four positions. While, in general, several amino acid residues having relatively very high or very low preferences for specific positions were found to be common to both the Z-Pro-Y-X and Z-R-Y-X sequences, many significant differences were found between the two sets of data, which are to be attributed to specific interactions arising from the presence of the proline residue.

The 310 Helical Conformation of the Amino Terminal Decapeptide of Suzukacillin. 270 MHz 'H NMR Evidence for Eight Intramolecular Hydrogen Bonds

The amino terminal suzukacillin decapeptide fragment, Boc-Aib-Pro-Val-Aib-Val-Ala-Aib-Ala-Aib-Aitbh-eO Me, two pentapeptides Boc-AibPrc-Val-AibVal-OMe and Boc-Ala-AibAla-AibAibOMe, and the tripeptide Boc-Ala-AibAibOMe have been studied by 270-MHz 'H NMR spectroscopy. By use of solvent dependence of chemical shifts in a CDC13-(CD3),S0 system and temperature dependence of amide NH chemical shifts in (CD3),S0, the intramolecularly hydrogen bonded NH groups in these peptides have been identified. The tripeptide possesses one hydrogen bond, both pentapeptides show evidence for three intramolecular hydrogen bonds, and the decapeptide has eight NH groups participating in hydrogen bonding. An Ala( 1)-Aib(2) @ turn is proposed for the tripeptide. Both pentapeptides favor 310 helical conformations composed of three consecutive B turns. The decapeptide adopts a 310 helical conformation with some flexibility at the Va1(5)-Ala(6) segment. The proposed conformations are consistent with the known stereochemical preferences of Aib residues.

Characterization of Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease, reveals a unique mode of DNA-binding, helical distortion and cleavage, compared to a canonical LAGLIDADG homing endonuclease

Mycobacterium leprae, which has undergone reductive evolution leaving behind a minimal set of essential genes, has retained intervening sequences in four of its genes implicating a vital role for them in the survival of the leprosy bacillus. A single in-frame intervening sequence has been found embedded within its recA gene. Comparison of M. leprae recA intervening sequence with the known intervening sequences indicated that it has the consensus amino acid sequence necessary for being a LAGLIDADG-type homing endonuclease. In light of massive gene decay and function loss in the leprosy bacillus, we sought to investigate whether its recA intervening sequence encodes a catalytically active homing endonuclease. Here we show that the purified M. leprae RecA intein (PI-MleI) binds to cognate DNA and displays endonuclease activity in the presence of alternative divalent cations, Mg2+ or Mn2+. A combination of approaches including four complementary footprinting assays such as DNase I, Cu/phenanthroline, methylation protection and KMnO4, enhancement of 2-aminopurine fluorescence and mapping of the cleavage site revealed that PI-MleI binds to cognate DNA flanking its insertion site, induces helical distortion at the cleavage site and generates two staggered double-strand breaks. Taken together, these results implicate that PI-MleI possess a modular structure with separate domains for DNA target recognition and cleavage, each with distinct sequence preferences. From a biological standpoint, it is tempting to speculate that our findings have implications for understanding the evolution of LAGLIDADG family of homing endonucleases

Lighting the way: Towards reducing misorientation of olive ridley hatchlings due to artificial lighting at Rushikulya, India

Sea-finding behavior in sea turtle hatchlings is modified by the visual cues provided by artificial beach front lighting. The consequent landward movement of hatchlings in response to coastal electric lighting reduces their survival rates. We assessed the potential impact of coastal lighting at Rushikulya, an important mass nesting site of the olive ridley sea turtle (Lepidochelys olivacea) in the Indian Ocean region. We examined the response of hatchlings to light characteristics in an experimental setup, as well as to the existing lighting regimes along the beach, using arena trials. Previous studies on other species indicate preferential orientation towards low wavelength and high intensity light. Our study confirms these preferences among hatchlings from the Indian Ocean population of olive ridleys. In addition we also found that wavelength and intensity could have an interactive effect upon hatchling orientation. Hatchlings at the study site respond both to visible point sources of light and to sheer glows of light. Though beach plantations of introduced Casuarina equisetifolia are generally considered to have negative impacts on sea turtle nesting beaches, we found that they acted as an effective light barrier when planted about 50 m away from the high tide line. We developed a model of the expected impact of artificial lighting on hatchling orientation during mass hatching events of previous years, and predict as much as 50% misorientation in some years. We also developed a map representing the misorientation of hatchlings due to artificial lighting based on arena trials in different regions of the beach. The results of the study helped identify focal areas for light management on the beach, which could be critical for the survival of this population.

Conformationally Restricted Nucleocyclitols: a Study into their Conformational Preferences and Supramolecular Architecture in the Solid State

With the intent of probing the feasibility of employing annulation as a tactic to engender axial rich conformations in nucleoside analogues, two adenine-derived, ``conformationally restricted'' nucleocylitols, 9 and 10, have been conceptualized as representatives of a hitherto unexplored class of nucleic acid base-cyclitol hybrids. A general synthetic strategy, with an inherent scope for diversification, allowed rapid functionalization of indane and tetralin to furnish 9 and 10 respectively in fair yield. Single-crystal X-ray diffraction analysis revealed that the two nucleocyclitols under study, though homologous, present completely dissimilar modes of molecular packing, marked, in particular, by the nature of involvement of the adenynyl NH2 group in the supramolecular assembly. In addition, the crystal structures of 9 and 10 also exhibit two different conformations of the functionalized cyclohexane ring. Thus, while the six-membered carbocycle in cyclopenta-annulated 9 exists in the expected chair (C) conformation that in cyclohexaannulated 10, which crystallizes as a dihydrate, shows an unusual twist-boat (TB) conformation. From a close analysis of the (HNMR)-H-1 spectroscopic data recorded for 9 and 10 in CD3OD, it was possible to put forth a putative explanation for the uncanny conformational preferences of crystalline 9 and 10.

Mutational analysis of active-site residues in the Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease: Asp(122) and Asp(193) are crucial to the double-stranded DNA cleavage activity whereas Asp(218) is not

Mycobacterium leprae recA harbors an in-frame insertion sequence that encodes an intein homing endonuclease (PI-MleI). Most inteins (intein endonucleases) possess two conserved LAGLIDADG (DOD) motifs at their ctive center. A common feature of LAGLIDADG-type homing endonucleases is that they recognize and cleave the same or very similar DNA sequences. However, PI-MleI is distinctive from other members of the family of LAGLIDADG-type HEases for its modular structure with functionally separable domains for DNA-binding and cleavage, each with distinct sequence preferences. Sequence alignment analyses of PI-MleI revealed three putative LAGLIDADG motifs; however, there is conflicting bioinformatics data in regard to their identity and specific location within the intein polypeptide. To resolve this conflict and to determine the active-site residues essential for DNA target site recognition and double-stranded DNA cleavage, we performed site-directed mutagenesis of presumptive catalytic residues in the LAGLIDADG motifs. Analysis of target DNA recognition and kinetic parameters of the wild-type PI-MleI and its variants disclosed that the two amino acid residues, Asp(122) (in Block C) and Asp(193) (in functional Block E), are crucial to the double-stranded DNA endonuclease activity, whereas Asp(218) (in pseudo-Block E) is not. However, despite the reduced catalytic activity, the PI-MleI variants, like the wild-type PI-MleI, generated a footprint of the same length around the insertion site. The D122T variant showed significantly reduced catalytic activity, and D122A and D193A mutations although failed to affect their DNA-binding affinities, but abolished the double-stranded DNA cleavage activity. On the other hand, D122C variant showed approximately twofold higher double-stranded DNA cleavage activity, compared with the wild-type PI-MleI. These results provide compelling evidence that Asp(122) and Asp(193) in DOD motif I and II, respectively, are bona fide active-site residues essential for DNA cleavage activity. The implications of these results are discussed in this report.