Abstract：
:Small open reading frames (smORFs) and their encoded microproteins play central roles in microbes. However, there is a vast unexplored space of smORFs within human-associated microbes. A recent bioinformatic analysis used evolutionary conservation signals to enhance prediction of small protein families. To facilitate the annotation of specific smORFs, we introduce SmORFinder. This tool combines profile hidden Markov models of each smORF family and deep learning models that better generalize to smORF families not seen in the training set, resulting in predictions enriched for Ribo-seq translation signals. Feature importance analysis reveals that the deep learning models learn to identify Shine-Dalgarno sequences, deprioritize the wobble position in each codon, and group codon synonyms found in the codon table. A core-genome analysis of 26 bacterial species identifies several core smORFs of unknown function. We pre-compute smORF annotations for thousands of RefSeq isolate genomes and Human Microbiome Project metagenomes and provide these data through a public web portal.
journal_name
Cell Host Microbejournal_title
Cell host & microbeauthors
Durrant MG,Bhatt ASdoi
10.1016/j.chom.2020.11.002subject
Has Abstractpub_date
2021-01-13 00:00:00pages
121-131.e4issue
1eissn
1931-3128issn
1934-6069pii
S1931-3128(20)30619-3journal_volume
29pub_type
杂志文章abstract：:The clinically silent Plasmodium liver stage is an obligatory step in the establishment of malaria infection and disease. We report here that expression of heme oxygenase-1 (HO-1, encoded by Hmox1) is upregulated in the liver following infection by Plasmodium berghei and Plasmodium yoelii sporozoites. HO-1 overexpress...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2008.04.003
更新日期：2008-05-15 00:00:00
abstract：:Animal-microbe facultative symbioses play a fundamental role in ecosystem and organismal health. Yet, due to the flexible nature of their association, the selection pressures that act on animals and their facultative symbionts remain elusive. Here we apply experimental evolution to Drosophila melanogaster associated w...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2018.06.001
更新日期：2018-07-11 00:00:00
abstract：:Recent reports indicate that both the inflammasome (Wlodarska et al., 2014) and autophagy (Patel et al., 2013) pathways in goblet cells control mucin secretion, defects in which are linked to difficulties in clearing pathogenic bacteria and maintaining intestinal homeostasis and control colitis. ...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2014.02.014
更新日期：2014-03-12 00:00:00
abstract：:RIG-I detects double-stranded RNA (dsRNA) to trigger antiviral cytokine production. Protein deamidation is emerging as a post-translational modification that chiefly regulates protein function. We report here that UL37 of herpes simplex virus 1 (HSV-1) is a protein deamidase that targets RIG-I to block RNA-induced act...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2016.10.011
更新日期：2016-12-14 00:00:00
abstract：:The intestinal immune system has to strike a delicate balance between initiating inflammatory responses against invading bacterial pathogens and avoiding their induction against microbiota colonizing the lumen. Adequate inflammatory responses against bacterial invasion result in the lumenal secretion of antimicrobial ...
journal_title：Cell host & microbe
pub_type： 杂志文章,评审
doi：10.1016/j.chom.2010.06.003
更新日期：2010-07-22 00:00:00
abstract：:Low pathogenic H7N9 influenza viruses have recently evolved to become highly pathogenic, raising concerns of a pandemic, particularly if these viruses acquire efficient human-to-human transmissibility. We compared a low pathogenic H7N9 virus with a highly pathogenic isolate, and two of its variants that represent neur...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2017.09.008
更新日期：2017-11-08 00:00:00
abstract：:Herpesviruses subvert immune cell activation by inhibiting NK cell receptor (NKG2D)-activating ligands such as MICB. A human cytomegalovirus microRNA was recently shown to repress MICB expression. Nachmani et al. (2009) extend this finding to two other human herpesviruses, providing evidence for a conserved functional...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2009.03.009
更新日期：2009-04-23 00:00:00
abstract：:Human noroviruses are a major cause of epidemic and sporadic gastroenteritis worldwide and can chronically infect immunocompromised patients. Efforts to develop effective vaccines and antivirals have been hindered by the uncultivable nature and extreme genetic diversity of human noroviruses. Although they remain a par...
journal_title：Cell host & microbe
pub_type： 杂志文章,评审
doi：10.1016/j.chom.2014.05.015
更新日期：2014-06-11 00:00:00
abstract：:Long before the cause was discovered, peptic ulcers were known to occur preferentially in individuals of certain blood groups. In this issue of Cell Host & Microbe, Moonens et al. (2016) perform structural analyses of the Helicobacter pylori adhesin BabA to determine how the bacteria discriminately bind different bloo...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2015.12.013
更新日期：2016-01-13 00:00:00
abstract：:Recent studies have revealed remarkable species specificity of the Toll-like receptors (TLRs) TLR11 and TLR12 and the immunity-related GTPase (IRG) proteins that are essential elements for detection and immune control of Toxoplasma gondii in mice, but not in humans. The biological and evolutionary implications of thes...
journal_title：Cell host & microbe
pub_type： 杂志文章,评审
doi：10.1016/j.chom.2014.01.004
更新日期：2014-02-12 00:00:00
abstract：:In this issue of Cell Host & Microbe, Wilmore et al. (2018) co-housed isogenic mouse populations, uncovering commensal bacteria-induced serum IgA and IgA-producing bone marrow plasma cells as critical components of resistance against sepsis. They further identified gut microbial taxa that may account for the induction...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2018.02.007
更新日期：2018-03-14 00:00:00
abstract：:Vibrio parahaemolyticus, a Gram-negative halophilic bacterium that causes acute gastroenteritis in humans, is characterized by two type III secretion systems (T3SS), namely T3SS1 and T3SS2. T3SS2 is indispensable for enterotoxicity but the effector(s) involved are unknown. Here, we identify VopV as a critical effector...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2011.08.014
更新日期：2011-10-20 00:00:00
abstract：:The intestinal microbiota is important for induction of inflammatory bowel disease (IBD). IBD is associated with complex shifts in microbiota composition, but it is unclear whether specific bacterial subsets induce IBD and, if so, whether their proportions in the microbiota are altered during disease. Here, we fulfill...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2011.04.009
更新日期：2011-05-19 00:00:00
abstract：:Efforts to prevent human immunodeficiency virus type 1 (HIV-1) infection would benefit from understanding the factors that govern virus neutralization by antibodies. We present a mechanistic model for HIV-1 neutralization that includes both virus and antibody parameters. Variations in epitope integrity on the viral en...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2013.10.006
更新日期：2013-11-13 00:00:00
abstract：:While there is growing appreciation that the microbiome regulates gut-brain signaling, the underlying mechanisms remain elusive. In this issue of Cell Host & Microbe, Bhattarai et al. (2018) identify bacteria-derived tryptamine as a ligand for the gut-epithelium-expressed GPCR 5-HT4 receptor, thereby functioning as a ...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2018.05.020
更新日期：2018-06-13 00:00:00
abstract：:It is currently unclear at which point during viral replication that RNA genomes are first recognized as nonself by the immune system. In this issue of Cell Host & Microbe, Weber et al. show that incoming nucleocapsid-bound genomes are sufficient to bind and activate innate immune sensors. ...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2013.02.012
更新日期：2013-03-13 00:00:00
abstract：:Proviral latency is a major barrier to a cure for HIV. In this issue of Cell Host & Microbe, Hataye et al. (2019) show that reactivation of HIV latency is a non-deterministic, highly stochastic (i.e., noisy) process and propose that stochastic transitions to exponential viral expansion require a critical threshold of ...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2019.11.010
更新日期：2019-12-11 00:00:00
abstract：:Lifestyle, obesity, and the gut microbiome are important risk factors for metabolic disorders. We demonstrate in 1,976 subjects of a German population cohort (KORA) that specific microbiota members show 24-h oscillations in their relative abundance and identified 13 taxa with disrupted rhythmicity in type 2 diabetes (...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2020.06.004
更新日期：2020-08-12 00:00:00
abstract：:Type III secretion systems (T3SS) are used by bacteria to deliver proteins into the cytoplasm of eukaryotic cells. Most studies of T3SS have focused on the role of these secretion systems in specific host interactions. However, there is increasing evidence to suggest that T3SS are also used in interactions with multip...
journal_title：Cell host & microbe
pub_type： 杂志文章,评审
doi：10.1016/j.chom.2007.10.004
更新日期：2007-11-15 00:00:00
abstract：:The mechanisms through which commensal bacterial populations cause inflammatory disease when shifted to dysbiotic community structures are poorly understood. Jiao et al. (2013) demonstrate that, in the case of inflammatory disease in the mouth, stimulation of the intracellular pattern recognition receptor Nod1 is a cr...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2013.05.001
更新日期：2013-05-15 00:00:00
abstract：:Autophagy provides a mechanism for cells to conserve nutrients, but was recently associated with immunity to intracellular pathogens. Here, Zhao et al. (2008) present direct in vivo evidence that autophagy is linked to macrophage control of Toxoplasma gondii and Listeria monocytogenes and highlights that this process ...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2008.10.008
更新日期：2008-11-13 00:00:00
abstract：:Bacterial CRISPR-Cas systems employ RNA-guided nucleases to destroy phage (viral) DNA. Phages, in turn, have evolved diverse "anti-CRISPR" proteins (Acrs) to counteract acquired immunity. In Listeria monocytogenes, prophages encode two to three distinct anti-Cas9 proteins, with acrIIA1 always present. However, the sig...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2020.04.001
更新日期：2020-07-08 00:00:00
abstract：:Intestinal reovirus infection can trigger T helper 1 (TH1) immunity to dietary antigen, raising the question of whether other viruses can have a similar impact. Here we show that the acute CW3 strain of murine norovirus, but not the persistent CR6 strain, induces TH1 immunity to dietary antigen. This property of CW3 i...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2018.10.004
更新日期：2018-11-14 00:00:00
abstract：:Defensins are naturally occurring antimicrobial peptides that disrupt bacterial membranes and prevent bacterial invasion of the host. Emerging studies indicate that certain defensins also block virus infection; however, the mechanism(s) involved are poorly understood. We demonstrate that human alpha-defensins inhibit ...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2007.12.001
更新日期：2008-01-17 00:00:00
abstract：:The complex microbial community residing within the intestine plays important roles in host defense. However, the impact of enteric infection and inflammation on this resident community has not been fully explored. In this issue of Cell Host & Microbe, Lupp and coworkers reveal that the composition of the intestinal m...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2007.07.006
更新日期：2007-08-16 00:00:00
abstract：:HIV-1 Env, a trimer of gp120-gp41 heterodimers, mediates membrane fusion after binding host receptor CD4. Receptor binding displaces V1V2 loops from Env's apex, allowing coreceptor binding and opening Env to enable gp41-mediated fusion. We present 3.54 Å and 4.06 Å cryoelectron microscopy structures of partially open ...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2018.09.003
更新日期：2018-10-10 00:00:00
abstract：:The inner colon mucus layer capacity to separate bacteria from the epithelium is dependent on bacterial colonizers signaling to the host epithelium. In this issue of Cell Host & Microbe, Wlodarska et al. (2017) demonstrate that the mucin-utilizing Peptostreptococcus russellii protects the host from inflammatory diseas...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2017.06.011
更新日期：2017-07-12 00:00:00
abstract：:Successful viruses must overcome the body's immune defenses. In this issue of Cell Host & Microbe, Goffinet et al. (2009) provide evidence that the host protein CD317, the target of the HIV Vpu protein, is part of an ancient innate immune response directed against budding viruses. ...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2009.02.002
更新日期：2009-03-19 00:00:00
abstract：:Cerebral malaria is a complication of Plasmodium falciparum infection characterized by sudden coma, death, or neurodisability. Studies using a mouse model of experimental cerebral malaria (ECM) have indicated that blood-brain barrier disruption and CD8 T cell recruitment contribute to disease, but the spatiotemporal m...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2014.04.008
更新日期：2014-05-14 00:00:00
abstract：:Hepatitis C virus (HCV) vaccine efforts are hampered by the extensive genetic diversity of HCV envelope glycoproteins E1 and E2. Structures of broadly neutralizing antibodies (bNAbs) (e.g., HEPC3, HEPC74) isolated from individuals who spontaneously cleared HCV infection facilitate immunogen design to elicit antibodies...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2018.10.009
更新日期：2018-11-14 00:00:00
