Detection of cross-links between FtsH, YidC, HflK/C suggests a linked role for these proteins in quality control upon insertion of bacterial inner membrane proteins

Little is known about the quality control of proteins upon integration in the inner membrane of Escherichia coli. Here, we demonstrate that YidC and FtsH are adjacent to a nascent, truncated membrane protein using in vitro photo cross-linking. YidC plays a critical but poorly understood role in the biogenesis of E. coli inner membrane proteins (IMPs). FtsH functions as a membrane chaperone and protease. Furthermore, we show that FtsH and its modulator proteins HflK and HflC copurify with tagged YidC and, vice versa, that YidC copurifies with tagged FtsH. These results suggest that FtsH and YidC have a linked role in the quality control of IMPs.     

Evolution of antiparallel two-domain membrane proteins: tracing multiple gene duplication events in the DUF606 family

X-ray crystallography has revealed that many integral membrane proteins consist of two domains with a similar fold but opposite (antiparallel) orientation in the membrane. The proteins are believed to have evolved by gene duplication and gene fusion events from a dual topology ancestral membrane protein, that adapted both orientations in the membrane and formed antiparallel homodimers. Here, we present a detailed analysis of the DUF606 family of bacterial membrane proteins that contains the entire collection of intermediate states of such an evolutionary pathway: single genes that would code for dual topology homodimeric proteins, paired genes coding for homologous proteins with a fixed but opposite orientation in the membrane that would form heterodimers, and fused genes that encode antiparallel two-domain fusion proteins. Two types of paired genes can be discriminated corresponding to the order in which the genes coding for the two oppositely oriented proteins occur in the operon. On the protein level, the heterodimers resulting from the two types of gene pairs are indistinguishable. In contrast, two types of fused genes corresponding to the two possible orders in which the oppositely oriented domains are present in the encoded proteins, do result in discernible types of proteins. The large number of genetic and protein states in the DUF606 family allowed for a detailed phylogenic analysis that revealed a total of nine independent duplication events in the DUF606 family, five of which resulted in paired genes, and four resulted in fused genes. Noticeably, there was no evidence for a sequential mechanism in which fusions evolve from a pair of genes. Rather, an evolutionary mechanism is proposed by which antiparallel two-domain proteins are the direct result of a gene duplication event. Combining the phylogeny of proteins and hosting microorganisms allowed for a reconstruction of the evolutionary pathway.     

Targeting of C-terminal (tail)-anchored proteins: understanding how cytoplasmic activities are anchored to intracellular membranes

A class of integral membrane proteins, referred to as ‘tail-anchored proteins’, are inserted into phospholipid bilayers via a single segment of hydrophobic amino acids at the C-terminus, thereby displaying a large functional domain in the cytosol. This membrane attachment strategy allows eukaryotic cells to position a wide range of cytoplasmic activities close to the surface of an intracellular membrane. Tail-anchored proteins often, but not always, demonstrate a selective distribution to specific intracellular organelles. This membrane-specific distribution is required for the large number of targeting proteins that are tail-anchored, but may or may not be critical for the numerous tail-anchored pro-apoptotic and anti-apoptotic proteins of the Bcl-2 family. Recent work has begun to address the mechanism for targeting tail-anchored proteins to their resident membranes, but questions remain. What targeting signals determine each protein's intracellular location? Are there receptors for these signals and, if so, how do they function? What steps are required to integrate tail-anchored proteins into the phospholipid bilayers? In this Traffic Interchange, we summarise what is known about tail-anchored proteins, and outline the areas that are currently under study.     

RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA

The annotation of noncoding RNA genes remains a major bottleneck in genome sequencing projects. Most genome sequences released today still come with sets of tRNAs and rRNAs as the only annotated RNA elements, ignoring hundreds of other RNA families. We have developed a web environment that is dedicated to noncoding RNA (ncRNA) prediction, annotation, and analysis and allows users to run a variety of tools in an integrated and flexible manner. This environment offers complementary ncRNA gene finders and a set of tools for the comparison, visualization, editing, and export of ncRNA candidates. Predictions can be filtered according to a large set of characteristics. Based on this environment, we created a public website located at http://RNAspace.org. It accepts genomic sequences up to 5 Mb, which permits for an online annotation of a complete bacterial genome or a small eukaryotic chromosome. The project is hosted as a Source Forge project (http://rnaspace.sourceforge.net/).     

预测蛋白质间相互作用的生物信息学方法

后基因组时代的研究模式,已从原来的序列-结构-功能转向基因表达-系统动力学-生理功能。建立蛋白质间相互作用的完全网络,即蛋白质相互作用组(interactome),将有助于从系统角度加深对细胞结构和功能的认识,并为新药靶点的发现和药物设计提供理论基础。一系列系统分析蛋白质相互作用的实验方法已经建立,近年来,出现了多种预测蛋白质相互作用的生物信息学方法,这些方法不仅是对传统实验方法的有价值的补充,而且能够扩展实验方法的预测范围;同时,在开发这些方法的过程中建立了一些重要的分子进化和分子生物学慨念。本文综述了9种生物信息学方法的原理、方法评估、存在的问题．并分析了这个领域的发展前景。     

微生物基因组研究进展

本综述了微生物全基因组测序的基本方法,数据收集和组装,序列缺口的填充、全基因组序列注释。同时对微生物基因组的研究现状和重大意义也作了简单概述。     

A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs

Prokaryote gene annotation is complicated by large numbers of short open reading frames (ORFs) that arise naturally from genetic code design. Historically, many hypothetical ORFs have been annotated as genes in microbes, usually with an arbitrary length threshold (e.g. greater than 100 codons). Given the use of such thresholds, what is the extent of genuine undiscovered short genes in the current sampling of prokaryote genomes? To assess rigorously the potential under-annotation of short ORFs with homology, we exhaustively compared the polyORFome--all possible ORFs in 64 prokaryotes (53 bacteria and 11 archaea) plus budding yeast--to itself and to all known proteins. The novelty of our analysis is that, firstly, sequence comparisons to/between both annotated and un-annotated ORFs are considered, and secondly a two-step disabled-homology filter is applied to set aside putative pseudogenes and spurious ORFs. We find that un-annotated homologous short ORFs (uhORFs) correspond to a small but non-negligible fraction of the annotated prokaryote proteomes (0.5-3.8%, depending on selection criteria). Moreover, the disabled-homology filter indicates that about a third of uhORFs correspond to putative pseudogenes or spurious ORFs. Our analysis shows that the use of annotation length thresholds is unnecessary, as there are manageable numbers of short ORF homologies conserved (without disablements) across microbial genomes. Data on uhORFs are available from http://pseudogene.org/polyo     

Arabidopsis genome analysis as exemplified by analysis of chromosome 4

During the last decade the small cruciferous plant Arabidopsis thaliana has become a model organism for flowering plants. Sequencing and analysis of the Arabidopsis genome is nearing completion. Beside an overview on methods and strategies for Arabidopsis genome analysis, a summary of the results from the first analysis is presented.This includes an overview on chromosomal organisation and topological features as well as a first comparison with other genomes.     

一个园艺植物基因组序列和注释的在线批量实时提取平台

目前, 大量园艺植物基因组测序已经完成或接近尾声, 它们的基因组序列和注释数据极大地促进了功能基因组学研究。为给科研人员提供批量下载特定的基因组区段序列和注释平台, 笔者开发了一个称为OBRRP的生物信息学工具。OBRRP具有提取葡萄(Vitis vinifera)、桃(Prunus persica)、草莓(Fragaria vesca)、黄瓜(Cucumis sativus)、西瓜(Citrullus lanatus)、番茄(Solanum lycopersicum)、甜橙(Citrus sinensis)、苹果(Malus x domestica)、猕猴桃(Actinidia chinensis)、马铃薯(Solanum tuberosum)、香蕉(Musa acuminata)和拟南芥(Arabidopsis thaliana) 12种植物基因组序列及注释数据的功能; 同时, 也具有扩展到其它Gbrowser浏览器架构的数据库功能。测试结果表明, OBRRP是一个快捷简便的在线、批量和实时提取工具, 其登录地址为http://bioinfo.jit.edu.cn/OBRRP/。     

泛素连接酶-底物选择关系的研究进展

泛素是一种包含76个氨基酸的小分子蛋白。泛素共价结合到底物的过程称为泛素化修饰。泛素化修饰过程是一个由级联的泛素激活酶、泛素结合酶和泛素连接酶所介导的复杂过程,泛素化修饰具有高效、ATP依赖、高度特异的特点。泛素化修饰与细胞周期调控、细胞凋亡、转录调控、DNA损伤修复等一系列生物学过程密切相关。在泛素化修饰过程中,泛素连接酶对底物的识别,是决定泛素化修饰特异性的关键环节。泛素连接酶底物识别的相关机制研究不断被报道,鉴定泛素连接酶底物的高通量方法也在不断的改进和发展。随着实验研究的不断深入,实验数据的不断产出,利用生物信息学进行泛素连接酶底物的研究也开始受到关注。对泛素连接酶识别底物的相关机制、高通量泛素连接酶底物的鉴定方法、泛素连接酶底物的生物信息学研究和生物信息学在泛素连接酶底物研究中的发展方向进行讨论。     

Discovering and detecting transposable elements in genome sequences

The contribution of transposable elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Here we review the diversity of innovative approaches to identify and annotate TEs in the post-genomic era, covering both the discovery of new TE families and the detection of individual TE copies in genome sequences. These approaches span a broad spectrum in computational biology including de novo, homology-based, structure-based and comparative genomic methods. We conclude that the integration and visualization of multiple approaches and the development of new conceptual representations for TE annotation will further advance the computational analysis of this dynamic component of the genome.     

Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences

With the rapid growth of sequence databases, there is an increasing need for reliable functional characterisation and annotation of newly predicted proteins. To cope with such large data volumes, faster and more effective means of protein sequence characterisation and annotation are required. One promising approach is automatic large-scale functional characterisation and annotation, which is generated with limited human interaction. However, such an approach is heavily dependent on reliable data sources. The SWISS-PROT protein sequence database plays an essential role here owing to its high level of functional information.     

lncRNAs功能注释和预测

随着测序技术的发展,在各种哺乳动物中发现越来越多的长非编码RNAs（long non-coding RNAs,lncRNAs）,但是大部分lncRNAs的功能却未知.鉴于lncRNAs在众多生物过程如免疫反应、发育和基因印迹中表现出对蛋白编码基因和其它非编码RNAs的重要调节作用,对lncRNAs的功能研究也成为生物学家和生物信息学家研究的热点. 其中,功能注释和预测是目前研究lncRNAs功能的主要方法之一.本文主要对lncRNAs功能注释和预测方法的研究进展作一综述,包括以下几个方面：基于共表达网络的方法、基于miRNAs的方法、基于蛋白质结合的方法、基于表观遗传修饰的方法以及基于ceRNA网络的方法. 为进一步研究lncRNAs的功能提供参考,同时为开发更加有效的注释或预测方法提供线索.     

Arginine 357 of SecY is needed for SecA-dependent initiation of preprotein translocation

The Escherichia coli SecYEG complex forms a transmembrane channel for both protein export and membrane protein insertion. Secretory proteins and large periplasmic domains of membrane proteins require for translocation in addition the SecA ATPase. The conserved arginine 357 of SecY is essential for a yet unidentified step in the SecA catalytic cycle. To further dissect its role, we have analysed the requirement for R357 in membrane protein insertion. Although R357 substitutions abolish post-translational translocation, they allow the translocation of periplasmic domains targeted co-translationally by an N-terminal transmembrane segment. We propose that R357 is essential for the initiation of SecA-dependent translocation only.