Predicting subcellular localization of proteins using machine-learned classifiers

MOTIVATION

Identifying the destination or localization of proteins is key to understanding their function and facilitating their purification. A number of existing computational prediction methods are based on sequence analysis. However, these methods are limited in scope, accuracy and most particularly breadth of coverage. Rather than using sequence information alone, we have explored the use of database text annotations from homologs and machine learning to substantially improve the prediction of subcellular location.

RESULTS

We have constructed five machine-learning classifiers for predicting subcellular localization of proteins from animals, plants, fungi, Gram-negative bacteria and Gram-positive bacteria, which are 81% accurate for fungi and 92-94% accurate for the other four categories. These are the most accurate subcellular predictors across the widest set of organisms ever published. Our predictors are part of the Proteome Analyst web-service.

Genomes of the parapoxviruses ORF virus and bovine papular stomatitis virus

Bovine papular stomatitis virus (BPSV) and orf virus (ORFV), members of the genus Parapoxvirus of the Poxviridae, are etiologic agents of worldwide diseases affecting cattle and small ruminants, respectively. Here we report the genomic sequences and comparative analysis of BPSV strain BV-AR02 and ORFV strains OV-SA00, isolated from a goat, and OV-IA82, isolated from a sheep. Parapoxvirus (PPV) BV-AR02, OV-SA00, and OV-IA82 genomes range in size from 134 to 139 kbp, with an average nucleotide composition of 64% G+C. BPSV and ORFV genomes contain 131 and 130 putative genes, respectively, and share colinearity over 127 genes, 88 of which are conserved in all characterized chordopoxviruses. BPSV and ORFV contain 15 and 16 open reading frames (ORFs), respectively, which lack similarity to other poxvirus or cellular proteins. All genes with putative roles in pathogenesis, including a vascular endothelial growth factor (VEGF)-like gene, are present in both viruses; however, BPSV contains two extra ankyrin repeat genes absent in ORFV. Interspecies sequence variability is observed in all functional classes of genes but is highest in putative virulence/host range genes, including genes unique to PPV. At the amino acid level, OV-SA00 is 94% identical to OV-IA82 and 71% identical to BV-AR02. Notably, ORFV 006/132, 103, 109, 110, and 116 genes (VEGF, homologues of vaccinia virus A26L, A33R, and A34R, and a novel PPV ORF) show an unusual degree of intraspecies variability. These genomic differences are consistent with the classification of BPSV and ORFV as two PPV species. Compared to other mammalian chordopoxviruses, PPV shares unique genomic features with molluscum contagiosum virus, including a G+C-rich nucleotide composition, three orthologous genes, and a paucity of nucleotide metabolism genes. Together, these data provide a comparative view of PPV genomics.

The genome of canarypox virus

Here we present the genomic sequence, with analysis, of a canarypox virus (CNPV). The 365-kbp CNPV genome contains 328 potential genes in a central region and in 6.5-kbp inverted terminal repeats. Comparison with the previously characterized fowlpox virus (FWPV) genome revealed avipoxvirus-specific genomic features, including large genomic rearrangements relative to other chordopoxviruses and novel cellular homologues and gene families. CNPV also contains many genomic differences with FWPV, including over 75 kbp of additional sequence, 39 genes lacking FWPV homologues, and an average of 47% amino acid divergence between homologues. Differences occur primarily in terminal and, notably, localized internal genomic regions and suggest significant genomic diversity among avipoxviruses. Divergent regions contain gene families, which overall comprise over 49% of the CNPV genome and include genes encoding 51 proteins containing ankyrin repeats, 26 N1R/p28-like proteins, and potential immunomodulatory proteins, including those similar to transforming growth factor beta and beta-nerve growth factor. CNPV genes lacking homologues in FWPV encode proteins similar to ubiquitin, interleukin-10-like proteins, tumor necrosis factor receptor, PIR1 RNA phosphatase, thioredoxin binding protein, MyD116 domain proteins, circovirus Rep proteins, and the nucleotide metabolism proteins thymidylate kinase and ribonucleotide reductase small subunit. These data reveal genomic differences likely affecting differences in avipoxvirus virulence and host range, and they will likely be useful for the design of improved vaccine vectors.

Acoustic response properties of lagenar nerve fibers in the sleeper goby, Dormitator latifrons

Auditory and vestibular functions of otolithic organs vary among vertebrate taxa. The saccule has been considered a major hearing organ in many fishes. However, little is known about the auditory role of the lagena in fishes. In this study we analyzed directional and frequency responses from single lagenar fibers of Dormitator latifrons to linear accelerations that simulate underwater acoustic particle motion. Characteristic frequencies of the lagenar fibers fell into two groups: </=50 Hz and 80-125 Hz. We observed various temporal response patterns: strong phase-locking, double phase-locking, phase-locked bursting, and non-phase-locked bursting. Some bursting responses have not been previously observed in vertebrate otolithic nerve fibers. Lagenar fibers could respond to accelerations as small as 1.1 mm s(-2). Like saccular fibers, lagenar fibers were directionally responsive and decreased directional selectivity with stimulus level. Best response axes of the lagenar fibers clustered around the lagenar longitudinal axis in the horizontal plane, but distributed in a diversity of axes in the mid-sagittal plane, which generally reflect morphological polarizations of hair cells in the lagena. We conclude that the lagena of D. latifrons plays a role in sound localization in elevation, particularly at high stimulus intensities where responses of most saccular fibers are saturated.

Effect of ligands that increase cAMP on caerulein-induced zymogen activation in pancreatic acini

The pathological activation of proteases within the pancreatic acinar cell is critical to initiating pancreatitis. Stimulation of acinar cells with supraphysiological concentrations of the CCK analog caerulein (CER) leads to protease activation and pancreatitis. Agents that sensitize the acinar cell to the effects of CCK might contribute to disease. The effects of physiological ligands that increase acinar cell cAMP [secretin, VIP, and pituitary adenylate cyclase activating peptide (PACAP)] on CER-induced responses were examined in isolated rat pancreatic acini. Each ligand sensitized the acinar cell to zymogen activation by physiological concentrations of CER (0.1 nM). VIP and PACAP but not secretin also enhanced activation by supraphysiological concentrations of CER (0.1 muM). A cell-permeable cAMP analog also sensitized the acinar cell to CER-induced activation. The cAMP antagonist Rp-8-Br-cAMP inhibited these sensitizing effects. These findings suggest that ligands that increase acinar cell cAMP levels can sensitize the acinar cell to the effects of CCK-induced zymogen activation.

Effect of Salvia Miltiorrhiza on coronary collateral circulation in dogs with experimental acute myocardial infarction

To evaluate the effect of Salvia Miltiorrhiza on coronary collateral circulation in dogs with experimental acute myocardial infarction, 12 dogs were randomly divided into Salvia Miltiorrhiza group (group D) and control group (group C). Acute myocardial infarction model was established in all dogs, Salvia Miltiorrhiza or saline was administered to the 2 groups respectively for 21 days. Coronary angiography was performed before and after ligation of coronary artery. The capillaries and distribution vessel density in tissue sections of myocardia were assessed. Angiography 2 h and 22 days after ligation of coronary artery revealed significant augmentation of collateral vessels, and capillaries and distribution vessel density in ischemic zone on day 22 showed statistically significant augmentation in group D as compared with that of controls (P < 0.05 and P < 0.01). It is concluded that Salvia Miltiorrhiza might improve the opening and formation of coronary collateral circulation of ischemic myocardia in dogs and thereby protecting myocardia from ischemia.

Genome of bovine herpesvirus 5

Here we present the complete genomic sequence of bovine herpesvirus 5 (BHV-5), an alphaherpesvirus responsible for fatal meningoencephalitis in cattle. The 138390-bp genome encodes 70 putative proteins and resembles the alpha2 subgroup of herpesviruses in genomic organization and gene content. BHV-5 is very similar to BHV-1, the etiological agent of infectious bovine rhinotracheitis, as reflected by the high level of amino acid identity in their protein repertoires (average, 82%). The highest similarity to BHV-1 products (>or=95% amino acid identity) is found in proteins involved in viral DNA replication and processing (UL5, UL15, UL29, and UL39) and in virion proteins (UL14, UL19, UL48, and US6). Among the least conserved ( Collapse

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MESH Headings

• Amino Acid Sequence
• Base Sequence
• Genes, Immediate-Early
• Genome, Viral
• Herpesvirus 5, Bovine/genetics
• Molecular Sequence Data
• Promoter Regions, Genetic
• Repetitive Sequences, Nucleic Acid
• Virus Latency/genetics

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DNA delivery from an intravascular stent with a denatured collagen-polylactic-polyglycolic acid-controlled release coating: mechanisms of enhanced transfection

We previously demonstrated that DNA-polylactic-polyglycolic acid (PLGA)-coated stents can deliver genes to the arterial wall with reporter expression involving 1% of neointimal cells. The present study investigated a novel formulation utilizing denatured collagen in DNA-stent coatings; denatured collagen was hypothesized to enhance gene transfer due to adhesion molecule interactions and actin-related mechanisms. Arterial smooth muscle cells (SMCs) cultivated on denatured collagen had significantly greater plasmid DNA (beta-galactosidase) transfection than SMC grown on native collagen (18.3+/-1.2 vs 1.0+/-0.1%, P<0.001). The denatured-collagen effect was completely blocked with anti-alpha(v)beta(3) integrin antibody. SMCs cultivated on native collagen supplemented with tenascin-C (TN-C), a protein recognized by alpha(v)beta(3) integrins, showed a 33-fold increase in transfection compared to control (P<0.001); this effect was also blocked with anti-alpha(v)beta(3) antibody. We observed that cells grown on denatured collagen had marked F-actin-enriched stress fibers and intense perinuclear G actin, compared to those grown on native collagen, which demonstrated F-actin-enriched focal adhesions without perinuclear G-actin localization. Cytochalasin-D, an F actin depolymerizing agent, caused significantly increased SMC transfection in cells cultivated on native collagen compared to control cells (18.0+/-1.8 vs 3.02+/-0.9%, P<0.001) further supporting the view that actin-related cytoskeletal changes influence transfection. A denatured-collagen-PLGA composite vascular stent coating similarly resulted in increased plasmid DNA green fluorescent protein (GFP) expression compared to controls (P<0.001) in SMC cultures; the increased transfection was blocked by anti-alpha(v)beta(3) antibody. Pig coronary studies comparing denatured-collagen-PLGA-coated stents containing plasmid DNA (encoding GFP) to coated stents without DNA demonstrated 10.8% of neointimal cells transfected; this level of expression was almost an order of magnitude greater than previously reported with a DNA delivery stent. It is concluded that denatured collagen incorporated into plasmid DNA-stent coating formulations may increase the level of gene expression in vitro and in vivo because of integrin-related mechanisms and associated changes in the arterial smooth muscle cell actin cytoskeleton.

The effect of frictional heating and forced cooling on the serum lubricant and wear of UHMW polyethylene cups against cobalt-chromium and zirconia balls

Hip simulator tests of femoral balls of cobalt-chromium alloy or zirconia against acetabular cups of UHMW polyethylene were run with and without a coolant circulated inside the femoral balls. Without cooling, the wear of polyethylene against zirconia was about 48% lower than with cobalt-chromium alloy, but the steady-state temperature of the zirconia ball was higher (55 degrees C vs. 41 degrees C), and there was more precipitation of protein from the serum, which sometimes formed an adherent layer on the surface of the zirconia. Circulating coolant at 1-20 degrees C markedly reduced the bearing temperatures and the protein precipitation. With coolant at 4 degrees C, wear of the polyethylene against cobalt-chromium alloy was about 26% lower than against zirconia, but the macroscopic and microscopic appearance of the worn polyethylene surfaces were unlike that typically generated in vivo. With or without coolant, the morphology of the polyethylene wear debris was comparable to that generated in vivo, but the ratio of fibrillar to granular debris was higher at the reduced temperature. These results suggested that circulating coolant at an appropriate temperature could avoid overheating (due to non-stop running of the simulator), preventing excessive protein precipitation while providing wear surfaces and wear debris with morphologies closely comparable to those generated in vivo.

Isolation and characterization of a Lactobacillus plantarum bacteriophage, phiJL-1, from a cucumber fermentation

A virulent Lactobacillus plantarum bacteriophage, PhiJL-1, was isolated from a commercial cucumber fermentation. The phage was specific for two related strains of L. plantarum, BI7 and its mutant (deficient in malolactate fermenting ability) MU45, which have been evaluated as starter cultures for controlled cucumber fermentation and as biocontrol microorganisms for minimally processed vegetable products. The phage genome of PhiJL-1 was sequenced to reveal a linear, double-stranded DNA (36.7 kbp). Sodium dodecyl sulfate-polyacryamide gel electrophoresis (SDS-PAGE) profiles indicated that PhiJL-1 contains six structural proteins (28, 34, 45, 50, 61, and 76 kDa). Electron microscopy revealed that the phage has an isometric head (59 nm in diameter), a long non-contractile tail (182 nm in length and 11 nm in width), and a complex base plate. The phage belongs to the Bradley group B1 or Siphoviridae family. One-step growth kinetics of the phage showed that the latent period was 35 min, the rise period was 40 min, and the average burst size was 22 phage particles/infected cell. Phage particles (90%) adsorbed to the host cells 20 min after infection. Calcium supplementation (up to 30 mM CaCl(2)) in MRS media did not affect the first cycle of phage adsorption, but promoted rapid phage propagation and cell lysis in the infection cycle subsequent to adsorption. The D values of PhiJL-1 at pH 6.5 were estimated to be 2.7 min at 70 degrees C and 0.2 min at 80 degrees C by a thermal inactivation experiment. Knowledge of the properties of L. plantarum bacteriophage PhiJL-1 may be important for the development of controlled vegetable fermentations.

Near-field scanning optical microscopy probes: a comparison of pulled and double-etched bent NSOM probes for fluorescence imaging of biological samples

Bent near-field optical probes for biological applications have been fabricated using a combination of a two-step chemical etching method and focused ion beam milling to create a well-defined aperture. The transmission efficiencies have been evaluated as a function of laser wavelength (lambda) and aperture size (D) for both large and small core fibres. The probe transmission behaviour follows a (D/lambda)3 relationship. The double-etched probes are compared to pulled probes fabricated from highly GeO2-doped dispersion compensating fibre and a standard single-mode optical fibre. The transmission efficiencies of both types of pulled probes are approximately two orders of magnitude lower than double-etched probes with similar aperture sizes. To demonstrate the utility of the various probes, their imaging performance has been evaluated for samples of polymer beads and phase-separated phospholipid monolayers of dipalmitoylphosphatidylcholine or cholesterol/phosphatidylcholine/sphingomyelin mixtures. Both pulled and double-etched probes are suitable for fluorescence imaging of polymer spheres. However, pulled probes are rapidly damaged at the higher input laser intensities required for fluorescence imaging of monolayer samples doped with < 1% of a fluorescent dye-labelled lipid. The images obtained with the double-etched probes show excellent spatial resolution and signal/noise, illustrating the potential of such probes for imaging of biological samples.

Comparative sequence analysis of the South African vaccine strain and two virulent field isolates of Lumpy skin disease virus

The genomic sequences of 3 strains of Lumpy skin disease virus (LSDV) (Neethling type) were compared to determine molecular differences, viz. the South African vaccine strain (LW), a virulent field-strain from a recent outbreak in South Africa (LD), and the virulent Kenyan 2490 strain (LK). A comparison between the virulent field isolates indicates that in 29 of the 156 putative genes, only 38 encoded amino acid differences were found, mostly in the variable terminal regions. When the attenuated vaccine strain (LW) was compared with field isolate LD, a total of 438 amino acid substitutions were observed. These were also mainly in the terminal regions, but with notably more frameshifts leading to truncated ORFs as well as deletions and insertions. These modified ORFs encode proteins involved in the regulation of host immune responses, gene expression, DNA repair, host-range specificity and proteins with unassigned functions. We suggest that these differences could lead to restricted immuno-evasive mechanisms and virulence factors present in attenuated LSDV strains. Further studies to determine the functions of the relevant encoded gene products will hopefully confirm this assumption. The molecular design of an improved LSDV vaccine is likely to be based on the strategic manipulation of such genes.

Bacteriophage ecology in commercial sauerkraut fermentations

Knowledge of bacteriophage ecology in vegetable fermentations is essential for developing phage control strategies for consistent and high quality of fermented vegetable products. The ecology of phages infecting lactic acid bacteria (LAB) in commercial sauerkraut fermentations was investigated. Brine samples were taken from four commercial sauerkraut fermentation tanks over a 60- or 100-day period in 2000 and 2001. A total of 171 phage isolates, including at least 26 distinct phages, were obtained. In addition, 28 distinct host strains were isolated and identified as LAB by restriction analysis of the intergenic transcribed spacer region and 16S rRNA sequence analysis. These host strains included Leuconostoc, Weissella, and Lactobacillus species. It was found that there were two phage-host systems in the fermentations corresponding to the population shift from heterofermentative to homofermentative LAB between 3 and 7 days after the start of the fermentations. The data suggested that phages may play an important role in the microbial ecology and succession of LAB species in vegetable fermentations. Eight phage isolates, which were independently obtained two or more times, were further characterized. They belonged to the family Myoviridae or Siphoviridae and showed distinct host ranges and DNA fingerprints. Two of the phage isolates were found to be capable of infecting two Lactobacillus species. The results from this study demonstrated for the first time the complex phage ecology present in commercial sauerkraut fermentations, providing new insights into the bioprocess of vegetable fermentations.

Prospective randomized comparison between redon catheters and chest tubes in drainage after cardiac surgery

AIM

To compare in a prospective randomized study chest tube (CT) and redon drains (RD) for effectiveness, cost, pain and complications after heart surgery using cardiopulmonary bypass.

METHODS

Forty patients undergoing heart surgery were analyzed prospectively. Twenty patients had small RD with strong (-700 mmHg) vacuum and 20 others standard CT. All patients had patient controlled analgesia in the postoperative period and pain was noted. Residual pericardial effusion (RPE) was controlled and quantified at postoperative day 7 with transthoracic echocardiography. Drainage complications were noted and compared in both groups.

RESULTS

Surgical statistics were comparable in both groups. Two patients underwent reoperation in CT for clotting, and 1 in RD for active surgical bleeding. One patient had orifice infection in CT. Drainage volumes and times were comparable in both groups at removal (992+/-507 ml in RD, 1154+/-571 ml in CT, p=ns). Morphine consumption and pain estimation were comparable in both groups in the postoperative period and at drainage removal. Echographic control showed important RPE for 3 patients in both groups. System cost was higher in CT compared to RD (up to 7 times).

CONCLUSION

RD are comparable to CT in terms of drainage, pain and complications. Nevertheless, they offer better handling and removal conditions and limited cost.

ETS2 is involved in protein kinase C-activated expression of granulocyte-macrophage colony-stimulating factor in human non-small lung carcinoma cell line, A549

Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a cytokine expressed in the non-small lung carcinoma cells (NSCLC). However, transcriptional regulation of GM-CSF is not well characterized in NSCLC. In this study we found that two cis-acting ETS family consensus sites are important for transcriptional regulation of GM-CSF in A549 human lung carcinoma cells. These two sites are located separately at around -40 and -100 bp from the transcription start site. Results of transient transfection assays with A549 cells indicated that ETS2 had a strong positive effect on GM-CSF promoter activity. Furthermore, this activity was enhanced by protein kinase C activator, phorbol 12-myristate 13-acetate (PMA), in an ETS consensus-dependent manner, while PMA could also enhance the expression level of ETS2. The protein kinase C inhibitors decreased GM-CSF promoter activity induced by the protein kinase C activator PMA. We also found that antisense ETS2 mRNA decreased PMA-induced GM-CSF promoter activity, supporting the possibility that ETS2 is involved in protein kinase C-induced GM-CSF transcriptional function. Endogenous expression of GM-CSF mRNA was increased by ETS2 transfection and the increased expression was further enhanced by PMA. These data indicate that GM-CSF is up-regulated by ETS2, a target of protein kinase C.

Effects of a red-tide toxin on fish hearing

Red tides are formed from blooms of marine algae. Among them, the dinoflagellate ( Karenia brevis) that is responsible for Florida red tides can release many types of natural toxins, which cause massive kills of marine animals, including endangered species, and threaten human health. This study was to investigate whether or not a neurotoxin, brevetoxin-3, purified from Florida red tides affects hearing sensitivity of a teleost fish, the goldfish ( Carassius auratus). LD(50) of the goldfish that were intraperitoneally injected with brevetoxin-3 was 0.068 microg g(-1). Evoked auditory brainstem responses were recorded, and hearing threshold was determined using a correlation method. By comparing thresholds of fish before and after a sublethal-dose injection (0.064 microg g(-1)) of the toxin, we found that brevetoxin-3 significantly reduces auditory sensitivity up to 9 dB at low frequencies (100 Hz and 500 Hz), but not at a high frequency (2,000 Hz). Reduction of hearing sensitivity was recovered within 24 h. To our knowledge, this is the first study showing a natural red-tide toxin causes minor hearing loss in vertebrates. Results of the study indicate that brevetoxin-3 could affect hearing capabilities of marine animals that survived exposure to red tides. Mechanisms of the toxin-induced reduction of hearing sensitivity are discussed.

Construction and identification of recombinant adenovirus vector containing the hVEGF165 gene

To construct the recombinant adenovirus vector containing the cDNA for human vascular endothelial growth factor (hVEGF165), the cDNA for hVEGF165 was subcloned into pACCMV.pLpA. Subsequently, this recombinant pACCMV.hVEGF was co-transfected into 293 cells together with pJM17 to obtain the replication-deficient recombinant adenovirus containing hVEGF gene--AdCMV.hVEGF. The VEGF gene expression was detected by using RT-PCR and Western blot in rabbit aorta vascular smooth muscle cells (VSMC) infected with AdCMV.hVEGF. Cultured human umbilical vein endothelial cells (HUVEC) were incubated with the conditioned medium (CM) from above mentioned VSMC infected with AdCMV.hVEGF to observe the effect of VEGF on proliferation of HUVEC. 48 h after the infection with AdCMV.hVEGF, VSMC demonstrated VEGF expression, and the expressed VEGF could stimulate the proliferation of HUVEC in vitro. Successfully prepared AdCMV.hVEGF165 could express biologically active VEGF in infected VSMC, and stimulate proliferation of HUVEC.

Effects of saccular otolith removal on hearing sensitivity of the sleeper goby (Dormitator latifrons)

It is not known to what extent the entire saccule contributes to overall hearing sensitivity in any fish species. Here we report directional and frequency sensitivity in a teleost fish (Dormitator latifrons) and effects of unilateral and bilateral removal of saccular otoliths on its hearing sensitivity. The fish had different hearing thresholds in the horizontal (-54.4 to -50.3 dB re: 1 micro m) and mid-sagittal (-58.6 to -53.1 dB) planes. At 100 Hz, unilateral otolith removal did not significantly change hearing sensitivity in the mid-sagittal plane, but caused selective reductions of auditory sensitivity by 3-7 dB in the azimuthal axes that are consistent with the longitudinal axis of the damaged saccule. Along the fish's longitudinal axis, unilateral otolith removal significantly decreased auditory sensitivity at 50 Hz and 400 Hz, but not at 100 Hz, 200 Hz, and 345 Hz. At 100 Hz, bilateral otolith removal resulted in robust hearing loss of 27-35 dB at different axes in both horizontal and mid-sagittal planes. Along the fish's longitudinal axis, the bilateral removal reduced auditory sensitivity by 13-27 dB at the different frequencies. Therefore, these results demonstrate that the saccule plays important roles in directional hearing and frequency responses.

Functional dissection of the ETS transcription factor MEF

We previously indicated that myeloid elf-1-like factor (MEF) but not elf-1, specifically activated lysozyme gene expression in epithelial cells. MEF is highly homologous at the nucleotide and amino acid level, with elf-1 especially in the ETS domain. Here, we report the functional analysis of the nuclear localization and transactivation properties of MEF. To investigate the intracellular localization of MEF, we transiently transfected MEF-green fluorescence protein (GFP) fusion protein expression vector into HeLa cells. A region spanning residues 177-291 is required for nuclear localization. We produced deletion mutants of MEF to determine the transactivation domain. The data showed that the N-terminal region, encompassing amino acids 1-52 is a potent transactivation domain. The C-terminal region spanning residues 477-663 can also mediate transactivation but not as strongly as the N-terminal region. The activity of the amino acid residues 1-52 was confirmed by experiments with fused constructs of MEF to the DNA binding-domain of the yeast GAL4 protein. These results, which determined the localization of the functional domains of MEF, will provide us with new clues to its transactivation mechanisms to regulate lysozyme gene expression in epithelial cells.

The genomes of sheeppox and goatpox viruses

Sheeppox virus (SPPV) and goatpox virus (GTPV), members of the Capripoxvirus genus of the Poxviridae, are etiologic agents of important diseases of sheep and goats in northern and central Africa, southwest and central Asia, and the Indian subcontinent. Here we report the genomic sequence and comparative analysis of five SPPV and GTPV isolates, including three pathogenic field isolates and two attenuated vaccine viruses. SPPV and GTPV genomes are approximately 150 kbp and are strikingly similar to each other, exhibiting 96% nucleotide identity over their entire length. Wild-type genomes share at least 147 putative genes, including conserved poxvirus replicative and structural genes and genes likely involved in virulence and host range. SPPV and GTPV genomes are very similar to that of lumpy skin disease virus (LSDV), sharing 97% nucleotide identity. All SPPV and GTPV genes are present in LSDV. Notably in both SPPV and GTPV genomes, nine LSDV genes with likely virulence and host range functions are disrupted, including a gene unique to LSDV (LSDV132) and genes similar to those coding for interleukin-1 receptor, myxoma virus M003.2 and M004.1 genes (two copies each), and vaccinia virus F11L, N2L, and K7L genes. The absence of these genes in SPPV and GTPV suggests a significant role for them in the bovine host range. SPPV and GTPV genomes contain specific nucleotide differences, suggesting they are phylogenetically distinct. Relatively few genomic changes in SPPV and GTPV vaccine viruses account for viral attenuation, because they contain 71 and 7 genomic changes compared to their respective field strains. Notable genetic changes include mutation or disruption of genes with predicted functions involving virulence and host range, including two ankyrin repeat proteins in SPPV and three kelch-like proteins in GTPV. These comparative genomic data indicate the close genetic relationship among capripoxviruses, and they suggest that SPPV and GTPV are distinct and likely derived from an LSDV-like ancestor.