TY - JOUR T1 - Primate transcript and protein expression levels evolve under compensatory selection pressures. JF - Science Y1 - 2013 A1 - Khan, Zia A1 - Ford, Michael J A1 - Cusanovich, Darren A A1 - Mitrano, Amy A1 - Pritchard, Jonathan K A1 - Gilad, Yoav KW - Animals KW - Evolution, Molecular KW - Gene Expression Regulation KW - HUMANS KW - Macaca mulatta KW - Pan troglodytes KW - Protein Biosynthesis KW - RNA, Messenger KW - Selection, Genetic KW - Species Specificity KW - Transcription, Genetic AB -

Changes in gene regulation have likely played an important role in the evolution of primates. Differences in messenger RNA (mRNA) expression levels across primates have often been documented; however, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are probably more important in determining phenotypic differences. We used high-resolution, quantitative mass spectrometry to collect protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines and compared them to transcript expression data from the same samples. We found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest that protein expression levels evolve under stronger evolutionary constraint than mRNA levels.

VL - 342 CP - 6162 M3 - 10.1126/science.1242379 ER - TY - Generic T1 - Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS. Y1 - 2012 A1 - Khan, Zia A1 - Bloom, Joshua S A1 - Amini, Sasan A1 - Singh, Mona A1 - Perlman, David H A1 - Caudy, Amy A A1 - Kruglyak, Leonid KW - Alleles KW - Chromatography, Liquid KW - Fungal Proteins KW - Gene Expression Profiling KW - Gene Expression Regulation, Fungal KW - HUMANS KW - Mass Spectrometry KW - proteomics KW - Regression Analysis KW - Saccharomyces KW - Saccharomyces cerevisiae KW - Saccharomyces cerevisiae Proteins KW - Species Specificity AB -

Understanding the genetic basis of gene regulatory variation is a key goal of evolutionary and medical genetics. Regulatory variation can act in an allele-specific manner (cis-acting) or it can affect both alleles of a gene (trans-acting). Differential allele-specific expression (ASE), in which the expression of one allele differs from another in a diploid, implies the presence of cis-acting regulatory variation. While microarrays and high-throughput sequencing have enabled genome-wide measurements of transcriptional ASE, methods for measurement of protein ASE (pASE) have lagged far behind. We describe a flexible, accurate, and scalable strategy for measurement of pASE by liquid chromatography-coupled mass spectrometry (LC-MS). We apply this approach to a hybrid between the yeast species Saccharomyces cerevisiae and Saccharomyces bayanus. Our results provide the first analysis of the relative contribution of cis-acting and trans-acting regulatory differences to protein expression divergence between yeast species.

JA - Mol Syst Biol VL - 8 M3 - 10.1038/msb.2012.34 ER - TY - JOUR T1 - The genome and its implications. JF - Adv Parasitol Y1 - 2011 A1 - Teixeira, Santuza M A1 - El-Sayed, Najib M A1 - Araújo, Patrícia R KW - Animals KW - Antigens, Protozoan KW - Chagas Disease KW - Chromosomes KW - Comparative Genomic Hybridization KW - DNA, Protozoan KW - Gene Expression Regulation KW - Genetic Variation KW - Genome, Protozoan KW - Host-Parasite Interactions KW - HUMANS KW - Species Specificity KW - Synteny KW - Transcription, Genetic KW - Transfection KW - Trypanosoma cruzi AB -

Trypanosoma cruzi has a heterogeneous population composed of a pool of strains that circulate in the domestic and sylvatic cycles. Genome sequencing of the clone CL Brener revealed a highly repetitive genome of about 110Mb containing an estimated 22,570 genes. Because of its hybrid nature, sequences representing the two haplotypes have been generated. In addition, a repeat content close to 50% made the assembly of the estimated 41 pairs of chromosomes quite challenging. Similar to other trypanosomatids, the organization of T. cruzi chromosomes was found to be very peculiar, with protein-coding genes organized in long polycistronic transcription units encoding 20 or more proteins in one strand separated by strand switch regions. Another remarkable feature of the T. cruzi genome is the massive expansion of surface protein gene families. Because of the high genetic diversity of the T. cruzi population, sequencing of additional strains and comparative genomic and transcriptome analyses are in progress. Five years after its publication, the genome data have proven to be an essential tool for the study of T. cruzi and increasing efforts to translate this knowledge into the development of new modes of intervention to control Chagas disease are underway.

VL - 75 M3 - 10.1016/B978-0-12-385863-4.00010-1 ER - TY - JOUR T1 - Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region. JF - BMC Genomics Y1 - 2006 A1 - Westenberger, Scott J A1 - Cerqueira, Gustavo C A1 - El-Sayed, Najib M A1 - Zingales, Bianca A1 - Campbell, David A A1 - Sturm, Nancy R KW - Amino Acid Sequence KW - Animals KW - Animals, Inbred Strains KW - Base Composition KW - Conserved Sequence KW - DNA, Kinetoplast KW - Frameshifting, Ribosomal KW - Gene Deletion KW - Gene Order KW - Genetic Variation KW - Leishmania KW - Models, Biological KW - Molecular Sequence Data KW - Muscle Proteins KW - NADH Dehydrogenase KW - Open Reading Frames KW - Regulatory Elements, Transcriptional KW - RNA Editing KW - Sequence Homology, Amino Acid KW - Species Specificity KW - Trypanosoma brucei brucei KW - Trypanosoma cruzi KW - Ubiquitin-Protein Ligases KW - Untranslated Regions AB -

BACKGROUND: The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification.

RESULTS: We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2.

CONCLUSION: The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network.

VL - 7 M3 - 10.1186/1471-2164-7-60 ER - TY - JOUR T1 - Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition JF - Journal of bacteriologyJournal of bacteriology Y1 - 2005 A1 - Joardar, Vinita A1 - Lindeberg, Magdalen A1 - Jackson, Robert W. A1 - J. Selengut A1 - Dodson, Robert A1 - Brinkac, Lauren M. A1 - Daugherty, Sean C. A1 - Deboy, Robert A1 - Durkin, A. Scott A1 - Giglio, Michelle Gwinn A1 - Madupu, Ramana A1 - Nelson, William C. A1 - Rosovitz, M. J. A1 - Sullivan, Steven A1 - Crabtree, Jonathan A1 - Creasy, Todd A1 - Davidsen, Tanja A1 - Haft, Dan H. A1 - Zafar, Nikhat A1 - Zhou, Liwei A1 - Halpin, Rebecca A1 - Holley, Tara A1 - Khouri, Hoda A1 - Feldblyum, Tamara A1 - White, Owen A1 - Fraser, Claire M. A1 - Chatterjee, Arun K. A1 - Cartinhour, Sam A1 - Schneider, David J. A1 - Mansfield, John A1 - Collmer, Alan A1 - Buell, C. Robin KW - Bacterial Proteins KW - DNA, Bacterial KW - Genes, Bacterial KW - Genome, Bacterial KW - Molecular Sequence Data KW - Pseudomonas syringae KW - Species Specificity KW - virulence AB - Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific. VL - 187 N1 - http://www.ncbi.nlm.nih.gov/pubmed/16159782?dopt=Abstract ER - TY - JOUR T1 - Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species JF - Nucleic acids researchNucleic Acids Research Y1 - 2004 A1 - Nelson, Karen E. A1 - Fouts, Derrick E. A1 - Mongodin, Emmanuel F. A1 - Ravel, Jacques A1 - DeBoy, Robert T. A1 - Kolonay, James F. A1 - Rasko, David A. A1 - Angiuoli, Samuel V. A1 - Gill, Steven R. A1 - Paulsen, Ian T. A1 - Peterson, Jeremy A1 - White, Owen A1 - Nelson, William C. A1 - Nierman, William A1 - Beanan, Maureen J. A1 - Brinkac, Lauren M. A1 - Daugherty, Sean C. A1 - Dodson, Robert J. A1 - Durkin, A. Scott A1 - Madupu, Ramana A1 - Haft, Daniel H. A1 - J. Selengut A1 - Van Aken, Susan A1 - Khouri, Hoda A1 - Fedorova, Nadia A1 - Forberger, Heather A1 - Tran, Bao A1 - Kathariou, Sophia A1 - Wonderling, Laura D. A1 - Uhlich, Gaylen A. A1 - Bayles, Darrell O. A1 - Luchansky, John B. A1 - Fraser, Claire M. KW - Base Composition KW - Chromosomes, Bacterial KW - DNA Transposable Elements KW - Food Microbiology KW - Genes, Bacterial KW - Genome, Bacterial KW - Genomics KW - Listeria monocytogenes KW - Meat KW - Open Reading Frames KW - Physical Chromosome Mapping KW - Polymorphism, Single Nucleotide KW - Prophages KW - Serotyping KW - Species Specificity KW - Synteny KW - virulence AB - The genomes of three strains of Listeria monocytogenes that have been associated with food-borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69 strain-specific genes were identified in L.monocytogenes strains F2365 (serotype 4b, cheese isolate), F6854 (serotype 1/2a, frankfurter isolate) and H7858 (serotype 4b, meat isolate), respectively. Eighty-three genes were restricted to serotype 1/2a and 51 to serotype 4b strains. These strain- and serotype-specific genes probably contribute to observed differences in pathogenicity, and the ability of the organisms to survive and grow in their respective environmental niches. The serotype 1/2a-specific genes include an operon that encodes the rhamnose biosynthetic pathway that is associated with teichoic acid biosynthesis, as well as operons for five glycosyl transferases and an adenine-specific DNA methyltransferase. A total of 8603 and 105 050 high quality single nucleotide polymorphisms (SNPs) were found on the draft genome sequences of strain H7858 and strain F6854, respectively, when compared with strain F2365. Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs. VL - 32 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15115801?dopt=Abstract ER - TY - JOUR T1 - The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. JF - Science Y1 - 2002 A1 - Dehal, Paramvir A1 - Satou, Yutaka A1 - Campbell, Robert K A1 - Chapman, Jarrod A1 - Degnan, Bernard A1 - De Tomaso, Anthony A1 - Davidson, Brad A1 - Di Gregorio, Anna A1 - Gelpke, Maarten A1 - Goodstein, David M A1 - Harafuji, Naoe A1 - Hastings, Kenneth E M A1 - Ho, Isaac A1 - Hotta, Kohji A1 - Huang, Wayne A1 - Kawashima, Takeshi A1 - Lemaire, Patrick A1 - Martinez, Diego A1 - Meinertzhagen, Ian A A1 - Necula, Simona A1 - Nonaka, Masaru A1 - Putnam, Nik A1 - Rash, Sam A1 - Saiga, Hidetoshi A1 - Satake, Masanobu A1 - Terry, Astrid A1 - Yamada, Lixy A1 - Wang, Hong-Gang A1 - Awazu, Satoko A1 - Azumi, Kaoru A1 - Boore, Jeffrey A1 - Branno, Margherita A1 - Chin-Bow, Stephen A1 - DeSantis, Rosaria A1 - Doyle, Sharon A1 - Francino, Pilar A1 - Keys, David N A1 - Haga, Shinobu A1 - Hayashi, Hiroko A1 - Hino, Kyosuke A1 - Imai, Kaoru S A1 - Inaba, Kazuo A1 - Kano, Shungo A1 - Kobayashi, Kenji A1 - Kobayashi, Mari A1 - Lee, Byung-In A1 - Makabe, Kazuhiro W A1 - Manohar, Chitra A1 - Matassi, Giorgio A1 - Medina, Monica A1 - Mochizuki, Yasuaki A1 - Mount, Steve A1 - Morishita, Tomomi A1 - Miura, Sachiko A1 - Nakayama, Akie A1 - Nishizaka, Satoko A1 - Nomoto, Hisayo A1 - Ohta, Fumiko A1 - Oishi, Kazuko A1 - Rigoutsos, Isidore A1 - Sano, Masako A1 - Sasaki, Akane A1 - Sasakura, Yasunori A1 - Shoguchi, Eiichi A1 - Shin-i, Tadasu A1 - Spagnuolo, Antoinetta A1 - Stainier, Didier A1 - Suzuki, Miho M A1 - Tassy, Olivier A1 - Takatori, Naohito A1 - Tokuoka, Miki A1 - Yagi, Kasumi A1 - Yoshizaki, Fumiko A1 - Wada, Shuichi A1 - Zhang, Cindy A1 - Hyatt, P Douglas A1 - Larimer, Frank A1 - Detter, Chris A1 - Doggett, Norman A1 - Glavina, Tijana A1 - Hawkins, Trevor A1 - Richardson, Paul A1 - Lucas, Susan A1 - Kohara, Yuji A1 - Levine, Michael A1 - Satoh, Nori A1 - Rokhsar, Daniel S KW - Alleles KW - Animals KW - Apoptosis KW - Base Sequence KW - Cellulose KW - Central Nervous System KW - Ciona intestinalis KW - Computational Biology KW - Endocrine System KW - Gene Dosage KW - Gene Duplication KW - genes KW - Genes, Homeobox KW - Genome KW - Heart KW - Immunity KW - Molecular Sequence Data KW - Multigene Family KW - Muscle Proteins KW - Organizers, Embryonic KW - Phylogeny KW - Polymorphism, Genetic KW - Proteins KW - Sequence Analysis, DNA KW - Sequence Homology, Nucleic Acid KW - Species Specificity KW - Thyroid Gland KW - Urochordata KW - Vertebrates AB -

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.

VL - 298 CP - 5601 M3 - 10.1126/science.1080049 ER - TY - JOUR T1 - Localization of sequences required for size-specific splicing of a small Drosophila intron in vitro. JF - J Mol Biol Y1 - 1995 A1 - Guo, M A1 - Mount, S M KW - Animals KW - Base Sequence KW - Cell Line KW - DNA KW - Drosophila KW - Genes, Insect KW - HeLa Cells KW - HUMANS KW - Introns KW - Molecular Sequence Data KW - Myosin Heavy Chains KW - RNA Splicing KW - Species Specificity AB -

Many introns in Drosophila and other invertebrates are less than 80 nucleotides in length, too small to be recognized by the vertebrate splicing machinery. Comparison of nuclear splicing extracts from human HeLa and Drosophila Kc cells has revealed species-specificity, consistent with the observed size differences. Here we present additional results with the 68 nucleotide fifth intron of the Drosophila myosin heavy chain gene. As observed with the 74 nucleotide second intron of the Drosophila white gene, the wild-type myosin intron is accurately spliced in a homologous extract, and increasing the size by 16 nucleotides both eliminates splicing in the Drosophila extract and allows accurate splicing in the human extract. In contrast to previous results, however, an upstream cryptic 5' splice site is activated when the wild-type myosin intron is tested in a human HeLa cell nuclear extract, resulting in the removal of a 98 nucleotide intron. The size dependence of splicing in Drosophila extracts is also intron-specific; we noted that a naturally larger (150 nucleotide) intron from the ftz gene is efficiently spliced in Kc cell extracts that do not splice enlarged introns (of 84, 90, 150 or 350 nucleotides) derived from the 74 nucleotide white intron. Here, we have exploited that observation, using a series of hybrid introns to show that a region of 46 nucleotides at the 3' end of the white intron is sufficient to confer the species-specific size effect. At least two sequence elements within this region, yet distinct from previously described branchpoint and pyrimidine tract signals, are required for efficient splicing of small hybrid introns in vitro.

VL - 253 CP - 3 M3 - 10.1006/jmbi.1995.0564 ER - TY - JOUR T1 - Species-specific signals for the splicing of a short Drosophila intron in vitro. JF - Mol Cell Biol Y1 - 1993 A1 - Guo, M A1 - Lo, P C A1 - Mount, S M KW - Animals KW - Base Sequence KW - Cell Nucleus KW - Consensus Sequence KW - DNA KW - DNA Transposable Elements KW - Drosophila KW - Drosophila Proteins KW - Electrophoresis, Polyacrylamide Gel KW - HeLa Cells KW - HUMANS KW - Introns KW - Molecular Sequence Data KW - Mutation KW - Peptide Hydrolases KW - Proteins KW - Regulatory Sequences, Nucleic Acid KW - Retroelements KW - RNA Splicing KW - Species Specificity AB -

The effects of branchpoint sequence, the pyrimidine stretch, and intron size on the splicing efficiency of the Drosophila white gene second intron were examined in nuclear extracts from Drosophila and human cells. This 74-nucleotide intron is typical of many Drosophila introns in that it lacks a significant pyrimidine stretch and is below the minimum size required for splicing in human nuclear extracts. Alteration of sequences of adjacent to the 3' splice site to create a pyrimidine stretch was necessary for splicing in human, but not Drosophila, extracts. Increasing the size of this intron with insertions between the 5' splice site and the branchpoint greatly reduced the efficiency of splicing of introns longer than 79 nucleotides in Drosophila extracts but had an opposite effect in human extracts, in which introns longer than 78 nucleotides were spliced with much greater efficiency. The white-apricot copia insertion is immediately adjacent to the branchpoint normally used in the splicing of this intron, and a copia long terminal repeat insertion prevents splicing in Drosophila, but not human, extracts. However, a consensus branchpoint does not restore the splicing of introns containing the copia long terminal repeat, and alteration of the wild-type branchpoint sequence alone does not eliminate splicing. These results demonstrate species specificity of splicing signals, particularly pyrimidine stretch and size requirements, and raise the possibility that variant mechanisms not found in mammals may operate in the splicing of small introns in Drosophila and possibly other species.

VL - 13 CP - 2 ER - TY - JOUR T1 - A catalogue of splice junction sequences. JF - Nucleic Acids Res Y1 - 1982 A1 - Mount, S M KW - Animals KW - Base Sequence KW - genes KW - Genes, Viral KW - HUMANS KW - Repetitive Sequences, Nucleic Acid KW - RNA Splicing KW - Species Specificity AB -

Splice junction sequences from a large number of nuclear and viral genes encoding protein have been collected. The sequence CAAG/GTAGAGT was found to be a consensus of 139 exon-intron boundaries (or donor sequences) and (TC)nNCTAG/G was found to be a consensus of 130 intron-exon boundaries (or acceptor sequences). The possible role of splice junction sequences as signals for processing is discussed.

VL - 10 CP - 2 ER - TY - JOUR T1 - Are snRNPs involved in splicing? JF - Nature Y1 - 1980 A1 - Lerner, M R A1 - Boyle, J A A1 - Mount, S M A1 - Wolin, S L A1 - Steitz, J A KW - Animals KW - Base Sequence KW - Cell Line KW - Chickens KW - Erythrocytes KW - HUMANS KW - Liver KW - Lupus Erythematosus, Systemic KW - Molecular Weight KW - Nucleic Acid Precursors KW - Nucleoproteins KW - Ribonucleoproteins KW - RNA, Heterogeneous Nuclear KW - Species Specificity VL - 283 CP - 5743 ER -